Ordered two- and three-dimensional structures of amphiphilic molecules

ABSTRACT

The invention pertains, at least in part, to a method for forming an ordered structure of amphiphilic molecules, such as proteins. The method includes contacting a population of amphiphilic molecules with a interface; compressing said population laterally to an appropriate pressure, such that an ordered structure at the interface is formed. The invention also pertains to the two- and three-dimensional ordered structures that are formed using the planar membrane compression method of the invention.

RELATED APPLICATION

This application is a divisional of U.S. application Ser. No.10/003,468, filed Oct. 23, 2001, which claims priority to U.S.Provisional Patent Application Ser. No. 60/242,913, entitled “ControlledFabrication of Crystals and Long-Range Ordered Arrays of MembraneProteins for High Throughput Structure Analysis and ScreeningApplications,” filed on Oct. 24, 2000; the entire contents of anypatents, patent applications, and references cited throughout thisspecification are hereby incorporated by reference in their entireties.

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BACKGROUND OF THE INVENTION

Protein structure information is indispensable for the design ofeffective drugs. Designers need detailed structures of proteins, toatomic resolution, so that they can tailor their drugs to interact withspecific target areas in a protein molecule. Conventionally, x-raycrystallography has been used to elucidate the three-dimensional (3-D)structure of proteins. This technique can accurately identify thelocation of atoms by diffracting x-rays from innumerable proteinmolecules stacked up in an ordered form, so called “crystal”. However,crystallographers have yet to overcome the fact that most proteins donot readily form ordered assemblies. Particularly important butextremely difficult to crystallize are membrane proteins. Membraneproteins are not soluble, therefore conventional three-dimensionalcrystallization techniques usually do not work for them.

To date, the number of transmembrane proteins crystallized remainssmall. Indeed, recently it was noted that only 26 out of theapproximately 1000 protein structure holdings in the Protein Data Bank(PDB) are membrane proteins (Nature Biotechnology 905 (2000)). In a 1998report of the Committee for the National

Magnetic Resonance Collaboration, it was stated that “even thoughmembrane proteins represent 30% of the proteome, relatively little isknown about the structure of these proteins, because of their resistanceto crystallization.”

In general, membrane proteins are comprised of hydrophobic portionswithin their transmembrane regions, which render them insoluble inwater. Consequently, unlike soluble proteins, membrane proteins do notform the monodispersed, isotropic solutions needed to grow crystals.This accounts for the near absence of structure information in PDB fortransmembrane portions of most membrane proteins. In contrast,extracellular domains of membrane proteins which lack the hydrophobicregions, have been successfully crystallized.

A few techniques have been developed for membrane proteincrystallization (Garavito, R. M. & Picot, D. Methods 1, 57-69 (1990);Kuelbrandt, W. Q. Rev. Biophysics 25, 1-49 (1992)). These techniquesinclude i) application of conventional three-dimensional crystallizationtechniques directly to a preparation of detergent-solubilized membraneprotein, e.g., by adding precipitation agents like ammonium sulfate orpolyethylene glycol; and (ii) reconstitution of membrane proteins intolipid bilayers by detergent removal. In both of these methods, thecrystallization process is hindered by the presence of detergent. Forexample, the detergent may inhibit crystal nucleation and growth. Thepresence of the detergent may require time-consuming and exhaustivedetergent screening to determine whether the solubilized protein isfunctionally active. Furthermore, the crystals may include thedetergent, therefore different detergents may yield different crystalsof the same protein. Detergents also may effect protein orientation;i.e. alternating molecules face up or down or two layers stack up withan in plane axis of two-fold symmetry. Furthermore, the processesinvolving detergents are tedious and require long crystallization times,(e.g., typically several days to several weeks). In addition, thesemethods require large quantities (several 100 milligrams to grams) ofpurified protein that is not easily available in most cases. Also,designing crystallization experiments for a new system is not straightforward, as the same protocol does not always work for other systems.

Recently Landau and Rosenbusch demonstrated formation ofthree-dimensional crystals of bacteriorhodopsin by emulating the naturalenvironment of the membrane protein in bicontinuous lipidic cubic phases(Landau, E. M. & Rosenbusch, J. P. Proc. Natl. Acad. Sci. USA 93 ,14532-14535 (1996)). Their method included a protein delipidationprocess and required the use of detergents and precipitants. Thecrystals produced by this method were small, 20-40 μm in diameter and 5μm thick, but diffracted x-rays from an intense microbeam source to 2.5Å resolution. These harsh conditions may adversely affect the structureand function of more vulnerable membrane proteins. Furthermore, theirmethod requires designing and building an artificial membrane with adifferent lattice size for each membrane protein. This does not appearto be an easy task.

Planar biological membranes are becoming of increasing interest becausethey provide a natural fluid membrane milieu that is criticallyimportant to the function of membrane proteins. This environment isideal for immobilizing proteins under nondenaturing conditions and in awell-defined orientation. Two-dimensional crystallization of solubleproteins on lipid monolayers has been attempted for several systems(Kornberg, R. D. & Darst, S. A. Curr. Opinion in Struct. Biol. 1,642-646 (1991); Newman, R. Electron Microscopy Reviews (1991)).Formation of two-dimensional crystals of non-soluble integral membraneproteins by compression of a monolayer at an air-water interface, hasnot yet been explored. Glaeser demonstrated preparation of thin, flatelectron microscopy specimen from monolayers spread at the air-waterinterface of a monolayer trough, from native purple membranes includingnaturally occurring two-dimensional crystals of bacteriorhodopsin(Glaeser, R. A. Ann. Rev. Phys. Chem. 36, 243-75 (1985)).

In phospholipid systems, finite two-dimensional domains have beenproduced by monolayer compression at an air-water interface for severallipids. In studies concerning the compression of the lipid DPPC inmonolayers, the presence of long-range orientational order throughoutthe solid domains produced at the coexistence region between two phaseswas found (Moy, V. T. et al. J. Phys. Chem. 92, 5233 (1988)). Theexperimental approach used in these studies does not provide concreteevidence on the crystalline order of the solid domains. However, theevidence of this long-range orientational order together withtheoretical analysis of structure formation in lipid monolayers mayprovide a basis for understanding the production of structures in morecomplex mixed lipid-protein monolayer systems (McConnell, H. M. Annu.Rev. Phys. Chem. 42, 171-95 (1991)).

SUMMARY OF THE INVENTION

The invention pertains, at least in part, to a new, simple and fastmethod for the fabrication of ordered structures, e.g., ordered two- andthree-dimensional crystals, of amphiphilic molecules, such as but notlimited to proteins, e.g., membrane proteins. Unlike conventionaltechniques, the methods of the invention allow for variation of theexperimental parameters to facilitate fabrication of ordered structureswith both long- as well as short-range orientation order, suitable forimaging techniques, such as high-resolution crystallographic analysis.In addition, the method is several times faster than conventionaltechniques, and maintains the native asymmetry of the amphiphilicmolecule. The methods of the invention provide a general approach forcrystallizing amphiphilic molecules such as membrane proteins. This isof considerable research interest since membrane proteins comprise ahigh proportion of pharmaceutically relevant targets. Yet thedifficulties involved in crystallizing membrane proteins by usingconventional techniques has posed a serious problem in the area of drugdiscovery. The present invention may lead to new discoveries ofsignificant biotechnological importance.

In an embodiment, the invention pertains, at least in part, to a methodfor forming an ordered structure of amphiphilic molecules. The methodincludes contacting a population of amphiphilic molecules with ainterface; compressing said population laterally to an appropriatepressure, such that an ordered structure at the interface is formed.

In a further embodiment, the invention pertains to two-dimensionalordered structures, which are comprised of a population of amphiphilicmolecules. The invention also pertains to three-dimensional orderedstructures which are formed by planar membrane compression, e.g., bycontacting a population of amphiphilic molecules with a interface; andcompressing the population to an appropriate pressure, such that athree-dimensional ordered structure is formed.

The invention also pertains, at least in part, to methods for screeninga test compound. The method includes contacting the test compound withat least a portion of an ordered structure; and analyzing the results ofthe interaction of the test compound and the ordered structure, suchthat said test compound is screened.

The invention also pertains, at least in part, to a method for thediscovering new leads. The method includes development of novel highthroughput screening systems based on structure-activity relationships.The method comprises a rapid fluorescence imaging method to probe themolecular outline of membrane proteins at low-resolutions (somewhatcomparable to that obtained from an electron diffraction projection dataat around 10-25 Å). This low-resolution imaging technique can be used asa powerful tool to not only probe the morphology of a protein but toalso depict probe changes in its conformation or degree of aggregationas a result of its interaction with other molecules. This is ofrelevance in biological molecular recognition events. A specificimplication of this technique is, for example, in signal transduction,where binding of molecular messengers to cell receptors, initiates aseries of complex events that generally include a change in conformationor multimerization, e.g., dimerization, of the protein.

The invention also pertains, at least in part, to a method fordetermining the shape of an amphiphilic molecule. The method includescontacting a population of the molecule with a interface; compressingthe population to an appropriate pressure, such that an orderedstructure is formed, and analyzing the ordered structure such that theshape of the amphiphilic molecule is determined.

A further application of the technology to probe structure informationat atomic scale resolutions is also presented. Structure information atatomic resolution is indispensable for elucidation of the mechanism ofaction of key membrane protein targets. Such information is crucial to abetter understanding of the nature of disease and subsequently todeveloping more effective drugs.

In another embodiment, the invention pertains, at least in part, to amethod for fabricating an ordered structure of a protein. The methodincludes expressing a protein in a cell, obtaining the protein from thecell, applying said protein to an interface, and compressing the proteinon the interface to an appropriate pressure.

In another embodiment, the invention includes a method for determiningthe structure of a protein. The method includes expressing the proteinin a cell, obtaining the protein from the cell, applying said protein toan interface, compressing said protein on said interface to anappropriate pressure, such that an ordered structure of said protein isformed, and analyzing said ordered structure such that the structure ofsaid protein is determined.

The invention also pertains to a protein chip. The chip includes aplurality of ordered structures in discrete wells, which are fabricatedby planar membrane compression.

In one embodiment, the invention pertains to methods for forming orderedstructures of amphiphilic molecules on an interface in a fast andcontrolled fashion. The methods may be performed using an apparatus withan integrated with real-time digital imaging laser fluorescencemicroscopy to allow for in-situ characterization of structure formation,throughout the fabrication process. The use of a robotics film transferfacilitates preparation of specimens for use in atomic resolutionmeasurements such as electron-, x-ray crystallography as well asscanning probe microscopy.

The inventions also pertains, at least in part, to a system for formingand analyzing a ordered structure of an amphiphilic molecules on ainterface. The system includes a trough comprising a frame having topand bottom separable frame portions, a plate for holding a interfacedisposed within said frame and including a substantially transparentportion; a seal assembly for sealing the subphase from the frame, and amovable barrier for laterally compressing a population of amphipilicmolecules deposited on said subphase to form an ordered structure; andan image acquisition and processing system coupled to the trough forimaging the ordered structure on the plate.

In yet another embodiment, the invention pertains, at least in part, toa system for forming an ordered structure of an amphiphilic molecule ona subphase. The system includes a trough comprising a frame having topand bottom separable frame portions, a plate disposed within said frameand including a transparent portion; a seal assembly for preventing thesubphase from reaching the frame, and a movable barrier for laterallycompressing a population of the amphiphilic molecules deposited on saidsubphase to form said ordered structure; and a housing enclosing thetrough; and a temperature control system for controlling the temperaturewithin the trough.

In yet another further embodiment, the invention also pertains to acomputer-readable medium for use in a system for forming and analyzingan ordered structure.

The computer readable medium includes instructions for performing thecomputer implemented steps of: viewing an ordered structure formed bycompression; and displaying an image of the ordered structure.

In yet another further embodiment, the invention also includes a troughfor forming and analyzing an ordered structure. The trough includes aframe having top and bottom separable frame portions, a plate forholding a subphase disposed within said frame and having an array ofmicrowells formed thereon for holding an array of ordered structures ofmembrane proteins; a seal assembly for sealing the subphase from theframe, and a movable barrier for laterally compressing a layer ofamphipilic solution deposited on said subphase to form an orderedstructure.

The methods and ordered structures of the invention provide many presentand potential applications, which range from fields such asmicroelectronics to biotechnology, agriculture, and food as well as fordevelopment of cosmetics, home and personal care products. Specifically,in biotechnology the invention has potential for developing moreeffective therapeutic treatments. Other applications include discoveryof active ingredients for use in food, cosmetics, home and personal careproducts. In agriculture, the methods of the invention may be used todesign more effective herbicides and insecticides.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 a is a top view of a plate mounted in a trough of theillustrative embodiment for developing discrete high-density proteinarrays according to the teachings of the invention.

FIG. 1 b is a cross-sectional view of the plate of FIG. 1 a.

FIG. 2 is a block diagram of the integrated trough system including andimage acquisition and processing system for viewing and analyzing asample formed in the trough according to the illustrative embodiment.

FIG. 3 a is a block diagram of a feedback control system for controllingthe temperature of the trough according to the illustrative embodiment.

FIG. 3 b is a schematic diagram of the temperature regulated housingsystem for controlling the temperature of a subphase in the trough ofthe illustrated embodiment.

FIGS. 4 a and 4 b are schematic diagrams of the electronics in thetemperature-regulated housing system of FIGS. 3 a and 3 b.

FIG. 5 is a block diagram of the software modules in the integratedtrough system of the illustrative embodiment.

FIG. 6 illustrates a graphical user interface generated for viewing andanalyzing a monolayer formed in the trough according to the illustrativeembodiment.

FIGS. 7A, 7C, and 7E are digital images representing ordered structuresgenerated by methods of the invention. FIGS. 7B, 7D, and 7F are digitalimages of the crystals of COX calculated from electron microscopyanalysis.

DETAILED DESCRIPTION OF THE INVENTION

One of the fastest-growing branches of materials chemistry is in thearea of planar mono- and multilayer films (Bell, C. M. et al. MaterialsChemistry of Organic Monolayer and Multilayer Thin Films (AmericanChemical Society, 1995)). The invention pertains, at least in part, to arapid process for controlled fabrication of ordered structures bycompression of a layer, e.g., a monolayer, of amphiphilic moleculestoward and beyond a critical density point. Experiments have beenconducted on three different model systems to elucidate application ofthe technology toward formation of two-dimensional as well asthree-dimensional ordered structures for: (1) the cytochrome c oxidase(COX), (2) the multidrug resistance P-glycoprotein (P-gp), both largemembrane spanning proteins having over 400 atoms and (3) cholesterol, asmall amphiphilic molecule. The results provide direct visual evidencefor the formation of interesting two-dimensional as well asthree-dimensional ordered structures.

Specifically, the two-dimensional ordered structures of cholesterolexhibit electron diffraction characteristics of highly orderedtwo-dimensional crystals. The diffraction pattern yields structureinformation to atomic resolution consistent with known data ofcholesterol monohydrate crystals prepared by conventional methods(Craven, B. M. Nature 260, 727-729 (1976)). Furthermore, these studiesreveal a direct correlation between the degree of supersaturation intwo-dimensions, beyond a metastable critical density point, and thecholesterol crystal nucleation process. The methods of the inventionprovide a two-dimensional framework for studying the underlying effectspromoting crystal nucleation process near a critical density point.

Digital fluorescence image analysis of the large two-dimensional orderedstructures of the membrane proteins COX and Pgp provide interestingunexpected insight into the long-range orientational order of proteinmolecules. These protein ordered structures exhibit a remarkablelong-range orientational order. The overall morphology of the orderedstructures often resembles the known structure of individual proteinmolecules in their monomer or dimer forms. The structural informationprovided by using this technique is somewhat comparable to that obtainedfrom low-resolution electron projection data around 10-25 Å.

1. Methods for Forming Two- and Three-Dimensional Ordered Structures

In one embodiment, the invention includes methods for forming orderedstructures. The methods include contacting a population of amphiphilicmolecules with a interface, compressing said population to anappropriate pressure, such that an ordered structure is formed. In afurther embodiment, the structure of the ordered structures may beelucidated using imaging techniques.

In comparison to conventional techniques of three dimensionalcrystallization, the methods of the invention are simple, fast (severalminutes vs. days and months) and require only a small amount of material(a fraction of a milligram vs. grams of the protein). In addition, theamphiphilic molecules can be ordered in theirs natural environmentwithout using detergents or solubilizing agents. For example, it isbelieved that in its natural environment the an amphiphilic molecule,such as a protein, is more likely to resume its function as well as itsnative conformational state, than it would in a solubilized orreconstituted form. Furthermore, the methods of the invention do notrequire the use of a highly purified protein. Instead, the process canbe adapted to form ordered structures of amphiphilic molecules, such asproteins, from small quantities of a crude preparations, such as crudemembrane preparations. This is of considerable advantage for membraneproteins, since most membrane proteins are not readily available inlarge quantities and it is even more difficult to find them in apurified form. However, for those proteins whose genes are known, smallquantities of a crude membrane form may be prepared, by overexpressingthe protein in cell cultures. It is anticipated that by overcoming thelimitations imposed by conventional methods, this unique and simpleapproach has the clear potential to be adopted as a general means toproduce ordered structures of amphiphilic molecules, such as membraneproteins, in a fast and cost-effective manner.

The term “ordered structures” includes ordered arrays and crystallinearrays of amphiphilic molecules. The ordered structures may be twodimensional (e.g., a single layer of amphiphilic molecules) or threedimensional (e.g., two or more layers of amphiphilic molecules). Orderedstructures can be analyzed by imaging techniques known in the art. In anembodiment, the ordered structures may be crystalline, and can beanalyzed by appropriate imaging or diffraction techniques, e.g.,electromagnetic radiation diffraction, to determine the shape orstructure of the amphiphilic molecule. The term includes nanostructuresand microstructures. The term includes both three-dimensional andtwo-dimensional crystals. In an embodiment, the ordered structure iscomprised of a population of similar, advantageously identical,molecules.

The term “imaging” or “imaging techniques” includes methods known in theart using any form of electromagnetic radiation, neutrons, includingtechniques such as absorption, fluorescence, reflectance, diffraction,scattering and includes illumination techniques such as transmission,reflectance, incident-light fluorescence, confocal, evanescent wave(including total internal reflection fluorescence and surface plasmonresonance), near field, multi-photons, interference, polarized light,chemi-luminescence and scanning probe microscopy techniques such asconfocal, atomic force and tunneling.

The term “crystalline array” includes arrays which diffractelectromagnetic radiation, e.g., x-rays, neutrons, light, etc.Crystalline arrays can be either two- or three-dimensional.

The term “diffraction of electromagnetic radiation” includes todiffraction by any source of radiation known to those in the art, suchas, but not limited to, neutrons, electromagnetic waves such as X-rays,electrons introduced from an x-ray tube, and focused and collimatedbeams of a synchrotron source or an electron microscope. The term alsoincludes the reflection of the primary radiation by sets of parallelplanes within the unit cells of a crystal. For example, when a beam ofradiation shines on a crystal, it is scattered by the atoms in alldirections. In certain directions, these scattered rays reinforce eachother and add up to a diffracted beam.

The term “ordered array” includes arrays in which amphiphilic moleculesassume the same orientation within the array. Ordered arrays can beeither two or three dimensional.

The term “amphiphilic molecules” includes proteins, lipids,lipoproteins, steroids, cholesterol, or other molecules or derivativesthereof which can be applied to a interface, compressed, to yield anordered structure. In certain embodiments, the term amphiphilicmolecules do not include lipids.

The term “protein” includes both naturally occurring, mutant, modified,and labeled (e.g., polypeptides. The protein may be comprised of atleast one hydrophobic region on its surface. The protein is not watersoluble. In a further embodiment, the protein may be a membrane protein,and/or a cellular receptor.

The term “membrane protein” includes proteins which in their nativestate are associated with lipid membranes (e.g., nuclear membrane,cellular membrane, mitochondrial membranes, liposomal membranes,endoplasmic reticulum membranes, chloroplast membranes, etc.). The termincludes transmembrane proteins, and proteins which are partially orfully embedded in membranes in their native state. Examples of membraneproteins include G-protein coupled receptors (GPCRs), signaltransduction receptors, orphan receptors, and other cellular receptors.

The term “membrane proteins” include both extrinsic and intrinsicproteins. Extrinsic membrane proteins are generally located entirelyoutside of the membrane, but are bound to the membrane by weak molecularattractions (such as, for example, ionic, hydrogen, and/or Van der Waalsbonds). Intrinsic membrane proteins are, generally, embedded in themembrane. Intrinsic membrane proteins include, but are not limited toproteins which extend from one side of the membrane to the other, i.e.,transmembrane proteins. Examples of transmembrane proteins include, ionchannels and ion pumps. The term also includes glycoproteins whichcomprise carbohydrate sugars covalently attached to the protein. Atypical mammalian cell may have several hundred distinct types ofglycoprotein studding its plasma membrane.

Membrane proteins may comprise single transmembrane domains involvescertain membrane proteins that have multiple transmembrane domains. Acommonly used type of structure seen in many hundreds of serpentinetransmembrane proteins involves 7 hydrophobic domains inserted into theplasma membrane separated by hydrophilic regions that are looped outalternatively into either the cytoplasm or the extracellular space.

In one embodiment, the proteins of the invention include receptors.There are three general classes of cell-surface receptors based on theirmechanism of signal transduction; i.e. (1) ion-channel linked receptors,(2) enzyme-linked/catalytic receptors and (3) G protein-coupledreceptors involving second messenger molecules. These last two classesof receptor molecules have an extracellular domain that recognizes aspecific molecular signal (e.g., such as a cytokine), and atransmembrane domain that produces a response.

The term “receptor protein” or “receptor” includes any receptor whichinteracts with an extracellular molecule (i.e. hormone, growth factor,peptide) to modulate a signal in the cell. To illustrate the receptorcan be a cell surface receptor, or in other embodiments can be anintracellular receptor. In preferred embodiments, the receptor is a cellsurface receptor, such as: a receptor tyrosine kinase, e.g., an EPHreceptor; an ion channel; a cytokine receptor; an multi subunit immunerecognition receptor, a chemokine receptor; a growth factor receptor, ora G-protein coupled receptor, such as a chemoattracttractant peptidereceptor, a neuropeptide receptor, a light receptor, a neurotransmitterreceptor, or a polypeptide hormone receptor.

At least four families of hormone receptors can be defined on the basisof similarity in primary sequence, predicted secondary and tertiarystructure and biochemical function. These are thehaemopoietin/interferon receptor family, the receptor kinase family, thetumor necrosis factor (TNF)/nerve growth factor (NGF) receptor familyand the family of G-protein coupled, seven membrane-spanning receptors.Also included are orphan receptors for which no ligands have yet beenidentified.

In one embodiment, the membrane proteins of the invention are involvedin signal transduction pathways. Signal transduction by growth factors,hormones and neurotransmitters is initiated by ligand binding toreceptors located in the plasma membrane. The cell surface receptorresponds to its specific ligand by a change in its conformation (such asthe case of the G protein-coupled receptor beta adrenergic receptor) orby an induced dimerization (as in receptor dimerization in the case ofthe human growth factor receptors), multimerization or through formationof heteromeric complexes (as in the TGF β signaling through formation oftypes I and II serine/threonine kinase receptors).

Other proteins which can be used in the methods of the invention includeproteins of the haemopoietin/interferon receptor family (e.g., type Itransmembrane glycoproteins). Ligands that interact with these receptorsinclude interferons (IFNs)-α, -β, and -γ, interleukins (IL) -2, -3, -4,-5, -6, -7, -9, -10, -11, -13, leukaemia inhibitory factor (LIF),oncostatin-M (OSM), erythropoitin (EPO), ciliary neurotrophic factor(CNTF), growth hormone and prolactin. Homodimerization appears to be animportant feature of some cytokine receptors including those for growthhormone, prolactin, EPO and granulocyte colony-stimulating factor. Otherproteins which also may be used include members of the TNF/NGF receptorfamily, such as those which have been identified as type I and type IITNF receptors, as well as the p75 subunit of the NGF receptors. Theligands for the TNF/NGF family members exist as type II transmembraneproteins, as well as secreted regulators.

Other membrane proteins include ligand-gated ion channels, such asneurotransmitter receptors (e.g., acetylcholine receptors, glutamatereceptors, γ-aminobutyric acid (GABA) receptors, and glycine receptors).Other cellular receptors which can be used include, but are not limitedto, enzyme-linked/catalytic receptors which have enzymic activity (e.g.,a tyrosine-specific protein kinase such as the insulin receptor). Theproteins of the invention include proteins of the five known classes ofenzyme-linked/catalytic receptors: (1) receptor tyrosine kinases, whichphosphorylate specific tyrosine residues on intracellular signalingproteins; (2) tyrosine kinase-associated receptors such as the prolactinand growth hormone receptors, which associate with proteins that havetyrosine kinase activity; (3) receptor tyrosine phosphatases, whichremove phosphate groups from tyrosine residues of specific intracellularsignaling proteins; (4) transmembrane receptor serine/threonine kinases,which add a phosphate group to serine and threonine side chains ontarget proteins; and (5) transmembrane guanyl cyclases, which catalyzethe production of cyclic GMP in the cytosol. Tyrosine kinase domains areinvolved in a variety of diverse biological processes including cellgrowth, shape, cycle, transcription and apoptosis (programmed celldeath).

The term “orphan receptors” include receptors with no known ligand and,in certain embodiments, obscure biological function. Receptors of alltypes comprise this large family. A large number of orphan receptorshave been identified in the EPH family (Hirai et al (1987) Science238:1717-1720). HER3 and HER4 are orphan receptors in the epidermalgrowth factor receptor family (Plowman et al. (1993) Proc. Natl. Acad.Sci. USA 90:1746-1750). ILA is a newly identified member of the humannerve growth factor/tumor necrosis factor receptor family (Schwarz etal. (1993) Gene 134:295-298). IRRR is an orphan insulin receptor-relatedreceptor which is a transmembrane tyrosine kinase (Shier et al. (1989)J. Biol Chem 264:14606-14608). Several orphan tyrosine kinase receptorshave been found in Drosophila (Perrimon (1994) Curr. Opin. Cell Biol.6:260-266). Known orphan receptors include the nuclear receptorsCOUP-TF1/EAR3, COUP-TF2/ARP1, EAR-1, EAR-2, TR-2, PPAR1, HNF-4, ERR-1,ERR-2, NGFIB/Nur77, ELP/SF-1 and MPL (Parker et al, supra, and Power etal. (1992) TIBS 13:318-323).

One large subgroup of orphan receptors are found in the G proteincoupled receptor family. Approximately 100 such receptors have beenidentified by function and these mediate transmembrane signaling fromexternal stimuli (vision, taste and smell), endocrine function(pituitary and adrenal), exocrine function (pancreas), heart rate,lipolysis, and carbohydrate metabolism. Structural and geneticsimilarities suggest that G protein-coupled receptor superfamily can besubclassified into five distinct groups: (i) amine receptors (serotonin,adrenergic, etc.); (ii) small peptide hormone (somatostatin, TRH, etc.);(iii) large peptide hormone (LH-CG, FSH, etc.); (iv) secretin family;and (v) odorant receptors (Buck L. and Axel, R. (1991) Cell 65:175-187),with orphan receptors apparently occurring in each of the sub-families.

Examples of G protein coupled receptors (“GPCRs”) include α1A-adrenergicreceptor, α1B-adrenergic receptor, α2-adrenergic receptor,α2B-adrenergic receptor, β1-adrenergic receptor, β2-adrenergic receptor,β3-adrenergic receptor, m1 acetylcholine receptor (AChR), m2 AChR, m3AChR, m4 AChR, m5 AChR, D1 dopamine receptor, D2 dopamine receptor, D3dopamine receptor, D4 dopamine receptor, D5 dopamine receptor, A1adenosine receptor, A2b adenosine receptor, 5-HT1a receptor, 5-HT1breceptor, 5HT1-like receptor, 5-HT1d receptor, 5HT1d-like receptor,5HT1d beta receptor, substance K (neurokinin A) receptor, fMLP receptor,fMLP-like receptor, angiotensin II type 1 receptor, endothelin ETAreceptor, endothelin ETB receptor, thrombin receptor, growthhormone-releasing hormone (GHRH) receptor, vasoactive intestinal peptidereceptor, oxytocin receptor, somatostatin SSTR1 and SSTR2, SSTR3,cannabinoid receptor, follicle stimulating hormone (FSH) receptor,leutropin (LH/HCG) receptor, thyroid stimulating hormone (TSH) receptor,thromboxane A2 receptor, platelet-activating factor (PAF) receptor, C5aanaphylatoxin receptor, Interleukin 8 (IL-8) IL-8RA, IL-8RB, DeltaOpioid receptor, Kappa Opioid receptor, mip-1/RANTES receptor,Rhodopsin, Red opsin, Green opsin, Blue opsin, metabotropic glutamatemGluR1-6, histamine H2 receptor, ATP receptor, neuropeptide Y receptor,amyloid protein precursor receptor, insulin-like growth factor IIreceptor, bradykinin receptor, gonadotropin-releasing hormone receptor,cholecystokinin receptor, melanocyte stimulating hormone receptor,antidiuretic hormone receptor, glucagon receptor, andadrenocorticotropic hormone II receptor.

Examples of membrane proteins include G Protein-Coupled Receptors(GPCRs), which constitute one of the largest superfamilies of proteins.The transmembrane region of the GPCRs contain seven helices eachspanning the lipid bilayer of the plasma membrane. When bound tospecific ligands, signals transmitted to the intracelluar domain ofthese receptors are amplified by a family of heterotrimeric guaninenucleotide-binding proteins (G proteins). G proteins act as molecularswitches that are activated by binding GTP and are inactivated when theGTP is hydrolyzed to GDP. The heterotrimeric G proteins consist of an α,β, and γ subunits.

GPCRs play key roles in a large number of pathophysiological conditionsand trigger several important physiological responses, including vision,smell, and stress. They are targets of numerous therapeutic drugs,including the nonselective α- and β-adrenergic agonists and antagonists,histamine antagonists, angiotensin antagonists, and serotoninantagonsists. The human genome is estimated to consist of over 1,000GPCR genes. In addition, the human genome contains numerous genes fordifferent α, β, and γ subunits to allow for the formation of hundreds ofdifferent G proteins. Consequently, there is a very large number ofpossible combinations of these receptors and G proteins, which providethe potential for development of a variety of clinically useful drugs.

Currently high-resolution structures are not available for any GPCR;although the structure of rhodopsin has been determined by electroncrystallography. Metal binding sites can provide information about GPCRstructure and activity or the dynamic conformational changes thataccompany receptor activation. Detailed knowledge about the molecularstructure of GPCRs is likely lead the development of new drugs withincreased specificity for distinct receptor subtypes and/or signaltransduction pathways.

Examples of physiological processes mediated by G proteins includeglycogen breakdown, visual excitation, histamine secretion in allallergic reactions, control of the rate of the heartbeat led by stimulussuch as epinephrine, light, IgE-antigen complexes, acetylcholine. Thesestimulant bind/affect the beta-adrenergic receptor, rhodopsin mast cellIgE receptor, and muscarinic receptor respectively.

Examples of EPH receptors include eph, elk, eck, sek, mek4, hek, hek2,eek, erk, tyrol, tyro4, tyro5, tyro6, tyro11, cek4, cek5, cek6, cek7,cek8, cek9, cek10, bsk, rtk1, rtk2, rtk3, myk1, myk2, ehk1, ehk2,pagliaccio, htk, erk and nuk receptors.

In another embodiment the receptor is a multisubunit receptor. Receptorscan be comprised of multiple proteins referred to as subunits, onecategory of which is referred to as a multisubunit receptor is a multisubunit immune recognition receptor (MIRR). MIRRs include receptorshaving multiple noncovalently associated subunits. MIRRs can include,but are not limited to, B cell antigen receptors, T cell antigenreceptors, Fc receptors and CD22, One example of an MIRR is an antigenreceptor on the surface of a B cell. The MIRR on the surface of a B cellcomprises membrane-bound immunoglobulin (mig) associated with thesubunits Ig-α and Ig-β or Ig-γ, which forms a complex capable ofregulating B cell function.

The term “population” includes two or more amphiphilic molecules whichare structurally similar or identical, such that diffraction techniquescan be used to determine the structure of the amphiphilic molecules. Inan advantageous embodiment, the population is comprised of identicalamphiphilic molecules.

The term “appropriate pressure” includes the amount of pressurenecessary for a particular protein to form a desired ordered structure,e.g., two dimensional or three dimensional ordered structure. In threedimensions, crystallization is promoted in a super-saturated solution.In two-dimensions, super-saturation translates into an increase in thelateral packing density of the molecules beyond a critical densitypoint. The Langmuir technique is used to organize the molecules at anair-aqueous interface and subsequently compress them in two-dimensionsto and beyond a critical density point. Examples of appropriatepressures include the pressures below the critical point fortwo-dimensional ordered structures and pressures at and above thecritical density point for three-dimensional ordered structures. Forexample, in an embodiment, the population of amphiphilic molecules arecompressed towards and beyond a critical density point, forming twodifferent groups of protein domains. Large (200-500 μm) orderedstructures are observed at intermediate packing densities, below thecritical point. At higher packing densities, beyond the critical densitypoint, formation of smaller (20-50 μm) ordered structures with a typicalappearance of a three dimensional crystal, may be observed usingappropriate techniques, e.g., fluorescence. Preferably, the pressure isapplied laterally (e.g., essentially parallel to the plane of theinterface) such that a ordered structure is formed.

The population of amphiphilic molecules may be compressed by any method,such that an ordered structure is formed. In certain embodiments, theappropriate pressure may be achieved by applying the amphiphilicmolecules to the interface and achieving the appropriate pressure toform an ordered structure of the invention without compression.

The term “interface” includes interfaces at which amphiphilic moleculescan be applied, such that an ordered structure is formed. Examples ofinterfaces include gas-liquid, gas-solid, liquid-gel, liquid-liquid,liquid-solid, etc. In a further embodiment, the interface isgas-aqueous. Examples of gases that may be used include those which donot adversely affect the formation of the ordered structures. Someexamples include gases such as argon, nitrogen, air, carbon dioxide,oxygen, etc. Examples of liquids that may be used include aqueoussolutions (e.g., buffer solutions, water, saline solutions, glycerinsolutions), organic solvents, or any other liquids which do notadversely affect the amphiphilic molecules or ordered structure.

The amphiphilic molecule may be contacted with the interface by anymethod which allows for the formation of the ordered structures of theinvention. Preferably, a population of amphiphilic molecules retaintheir native asymmetry or a uniform orientation. For protein amphiphilicmolecules, the proteins may be contacted with the interface in thepresence of a lipid membrane. For example, the proteins may be appliedto the interface in the presence of a cellular membrane of a cell wherethe protein was expressed or overexpressed. Protein also may be appliedto the interface in a liposome, proteoliposomes, a detergent solution,or by any method which allows for the formation of an ordered structureusing the methods of the invention. In a further embodiment when theamphiphilic molecule is a protein (such as, for example, a membraneprotein), the amphiphilic molecule is applied to the interface in apreparation which is essentially free of detergents (e.g., comprise lessthan about 0.1 or less percent detergent).

In a further embodiment, the method of the invention further comprisesthe formation of a planar membrane, comprised of at least theamphiphilic molecules, on the interface, prior to the formation of theordered structure.

The term “planar membrane” includes monolayers, bilayers, and othermembranes which are formed at the interface. The term “planar membrane”may be a monolayer, or bilayer, which when compressed, allows for theformation of ordered structures of populations of amphiphilic molecules.For example, amphiphilic molecules such as membrane proteins may beapplied to the interface in the presence of lipids. The lipids and theproteins then form a planar membrane which then is compressed to formthe protein ordered structures of the invention.

The invention pertains to methods of forming ordered structures ofamphiphilic molecules, such as, but not limited to, integral membraneproteins, by planar membrane compression, as an alternative strategy toconventional two-dimensional and three-dimensional crystallizationmethods. This method allows one to influence and control areorganization of membrane protein molecules within the monolayer tohigh packing densities necessary to induce nucleation and growth ofcrystals. Indeed, in some biological membranes ordered arrays have beenobserved simply from rearrangement of the protein within the membrane,either by removing the other membrane components or by induction with aspecific agent. For example, crystallization of the cytochrome c oxidasewas first observed accidentally during isolation and purification(Vanderkooi, G. et al. Biochim. Biophys. Acta 274, 38-48 (1972)).Crystallization upon reorganization has been particularly evident inbiological membranes containing high levels of only a few differentproteins at a high packing density.

Formation of two-dimensional ordered structures, e.g., two-dimensionalcrystallization, in planar membranes, in comparison with two-dimensionaland three-dimensional crystallization from solution has some advantages.The methods of the invention can be adapted to use small microgramquantities of the amphiphilic molecule such as proteins.

For proteins and other molecules associated with membranes in theirnative state, the methods of the invention are advantageous becausesince the protein does not dissociate from the lipid, it is likely thatthe native asymmetry of the protein will be maintained in the planarmembrane, i.e.; all proteins orienting in the same direction. Typically,proteins in two-dimensional crystals prepared from detergent solubilizedmembrane proteins resume a symmetrical orientation where alternatingprotein molecules face up and down.

In addition, in planar membranes, one can control and restrict thelateral mobility of the molecules of the planar membrane by varyingtheir packing density. This may increase the chances of latticeformation in comparison with crystallization from an isotropic solution.In bilayers, possibilities for improving the crystallization conditionsby varying experimental parameters are limited. In monolayerexperiments, depending of the spreading conditions, the protein isexposed to no or negligible levels of detergent and is therefore morestable. However, exposing large proportions of a protein molecule to airor water during spreading may cause denaturation of the protein. Proteindenaturation can be avoided by spreading the protein at a constantsurface pressure, in order to ensure an optimized packing density. Thepresence of other membrane components, in native membranes may sometimeslead to disordered ordered structures. Reconstituting purified proteinin the planar membrane can solve this problem. Alternatively, it can beminimized by using native membrane proteoliposome preparations includingover-expressed protein.

This controlled ordering of amphiphilic molecules to a large flatdomain, by compression, e.g., planar membrane compression, is suitablefor preparation of ordered structures of a particular amphiphilicmolecule for high-resolution atomic-scale structure analysis by electrondiffraction and other electromagnetic radiation diffraction techniquesknown in the art. It was hypothesized that preparation of large,well-ordered and flat specimen, to a tolerance of better than 1° over 1μm² range, could decrease broadening of the diffraction spots andtherefor provide better than 0.2 nm resolution (Glaeser, R. M. &Downing, K. H. Ultramicroscopy, 52, 478-486 (1993)).

The ability to form ordered ordered structures including, but notlimited to nanostructures and two-dimensional and three-dimensionalcrystals, on a liquid in a fast and controlled fashion has many presentand potential applications, which range from fields such asmicroelectronics, nonlinear optics to biotechnology, food, agriculture,cosmetics and home and personal care product development.

In a further embodiment, the invention pertains, at least in part, to amethod for fabricating an ordered structure of a protein. The methodincludes expressing said protein in a cell, obtaining said protein fromsaid cell, applying said protein to an interface, and compressing saidprotein on said interface to an appropriate pressure, such that anordered structure of said protein is formed.

In a further embodiment, the protein is over expressed in the cell. Inadvantageous embodiment, the protein is a membrane protein and is foundin a membrane of said cell. In a further embodiment, the protein isapplied to said interface in the presence of membrane lipids, e.g., in acrude membrane preparation. Examples of proteins which may be used inthe methods of the invention include, but are not limited to, membraneproteins, cellular receptors, orphan receptors, receptor tyrosinekinases, EPH receptors, ion channels, a cytokine receptors, multisubunitimmune recognition receptors, chemokine receptors, growth factorreceptors, or G-protein coupled receptors.

The term “over expressed” includes the enhancement in the amount of aparticular protein of interest expressed by a host cell, by culturing ina suitable medium a host cell (e.g., a mammalian host cell such as anon-human mammalian cell) containing a recombinant expression vector,such that the protein is produced.

As used herein, the term “vector” refers to a nucleic acid moleculecapable of transporting another nucleic acid to which it has beenlinked. One type of vector is a “plasmid”, which refers to a circulardouble stranded DNA loop into which additional DNA segments can beligated. Another type of vector is a viral vector, wherein additionalDNA segments can be ligated into the viral genome. Certain vectors arecapable of autonomous replication in a host cell into which they areintroduced (e.g., bacterial vectors having a bacterial origin ofreplication and episomal mammalian vectors). Other vectors (e.g.,non-episomal mammalian vectors) are integrated into the genome of a hostcell upon introduction into the host cell, and thereby are replicatedalong with the host genome. Moreover, certain vectors are capable ofdirecting the expression of genes to which they are operatively linked.Such vectors are referred to herein as “expression vectors”. In general,expression vectors of utility in recombinant DNA techniques are often inthe form of plasmids. In the present specification, “plasmid” and“vector” can be used interchangeably as the plasmid is the most commonlyused form of vector. However, the invention is intended to include suchother forms of expression vectors, such as viral vectors (e.g.,replication defective retroviruses, adenoviruses and adeno-associatedviruses), which serve equivalent functions.

The recombinant expression vectors comprise a nucleic acid containingthe sequence of the desired protein in a form suitable for expression ofthe nucleic acid in a host cell, which means that the recombinantexpression vectors include one or more regulatory sequences, selected onthe basis of the host cells to be used for expression, which isoperatively linked to the nucleic acid sequence to be expressed. Withina recombinant expression vector, “operably linked” is intended to meanthat the nucleotide sequence of interest is linked to the regulatorysequence(s) in a manner which allows for expression of the nucleotidesequence (e.g., in an in vitro transcription/translation system or in ahost cell when the vector is introduced into the host cell). The term“regulatory sequence” is intended to include promoters, enhancers andother expression control elements (e.g., polyadenylation signals). Suchregulatory sequences are described, for example, in Goeddel; GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990). Regulatory sequences include those which directconstitutive expression of a nucleotide sequence in many types of hostcells and those which direct expression of the nucleotide sequence onlyin certain host cells (e.g., tissue-specific regulatory sequences). Itwill be appreciated by those skilled in the art that the design of theexpression vector can depend on such factors as the choice of the hostcell to be transformed, the level of expression of polypeptide desired,and the like. The expression vectors of the invention can be introducedinto host cells to thereby produce proteins or peptides, includingfusion proteins or peptides, encoded by nucleic acids encoding thedesired protein to be expressed.

The recombinant expression vectors can be designed for expression of theproteins in prokaryotic or, advantageously, eukaryotic cells. Forexample, the proteins can be expressed in bacterial cells such as E.coli, insect cells (using baculovirus expression vectors) yeast cells ormammalian cells. Suitable host cells are discussed further in Goeddel,Gene Expression Technology: Methods in Enzymology 185, Academic Press,San Diego, Calif. (1990). Alternatively, the recombinant expressionvector can be transcribed and translated in vitro, for example using T7promoter regulatory sequences and T7 polymerase.

Expression of proteins in prokaryotes is most often carried out in E.coli with vectors containing constitutive or inducible promotersdirecting the expression of proteins. Examples of suitable inducible E.coli expression vectors include pTrc (Amann et al., (1988) Gene69:301-315) and pET 11d (Studier et al., Gene Expression Technology:Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990)60-89). Target gene expression from the pTrc vector relies on host RNApolymerase transcription from a hybrid trp-lac fusion promoter. Targetgene expression from the pET 11d vector relies on transcription from aT7 gn10-lac fusion promoter mediated by a coexpressed viral RNApolymerase (T7 gn1). This viral polymerase is supplied by host strainsBL21(DE3) or HMS174(DE3) from a resident prophage harboring a T7 gn1gene under the transcriptional control of the lacUV 5 promoter.

One strategy to maximize recombinant protein expression in E. coli is toexpress the protein in a host bacteria with an impaired capacity toproteolytically cleave the recombinant protein (Gottesman, S., GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990) 119-128). Another strategy is to alter the nucleicacid sequence of the nucleic acid to be inserted into an expressionvector so that the individual codons for each amino acid are thosepreferentially utilized in E. coli (Wada et al., (1992) Nucleic AcidsRes. 20:2111-2118). Such alteration of nucleic acid sequences of theprotein can be carried out by standard DNA synthesis techniques.

In another embodiment, the HST-4 and/or the HST-5 expression vector is ayeast expression vector. Examples of vectors for expression in yeast S.cerevisiae include pYepSec1 (Baldari, et al., (1987) Embo J. 6:229-234),pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz etal., (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego,Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).

Alternatively, the proteins can be expressed in insect cells usingbaculovirus expression vectors. Baculovirus vectors available forexpression of proteins in cultured insect cells (e.g., Sf 9 cells)include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165)and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).

In yet another embodiment, the protein is expressed in mammalian cellsusing a mammalian expression vector. Examples of mammalian expressionvectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC(Kaufman et al. (1987) EMBO J. 6:187-195). When used in mammalian cells,the expression vector's control functions are often provided by viralregulatory elements. For example, commonly used promoters are derivedfrom polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40. Forother suitable expression systems for both prokaryotic and eukaryoticcells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., andManiatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., ColdSpring Harbor Laboratory, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1989.

A host cell can be any prokaryotic or eukaryotic cell. For example, theprotein can be expressed in bacterial cells such as E. coli, insectcells, yeast or mammalian cells (such as Chinese hamster ovary cells(CHO) or COS cells). Other suitable host cells are known to thoseskilled in the art.

Vector DNA can be introduced into prokaryotic or eukaryotic cells viaconventional transformation or transfection techniques. As used herein,the terms “transformation” and “transfection” are intended to refer to avariety of art-recognized techniques for introducing foreign nucleicacid (e.g., DNA) into a host cell, including calcium phosphate orcalcium chloride co-precipitation, DEAE-dextran-mediated transfection,lipofection, or electroporation. Suitable methods for transforming ortransfecting host cells can be found in Sambrook, et al. (MolecularCloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989),and other laboratory manuals.

For stable transfection of mammalian cells, it is known that, dependingupon the expression vector and transfection technique used, only a smallfraction of cells may integrate the foreign DNA into their genome. Inorder to identify and select these integrants, a gene that encodes aselectable marker (e.g., resistance to antibiotics) is generallyintroduced into the host cells along with the gene of interest.Preferred selectable markers include those which confer resistance todrugs, such as G418, hygromycin and methotrexate. Nucleic acid encodinga selectable marker can be introduced into a host cell on the samevector as that encoding the protein or can be introduced on a separatevector. Cells stably transfected with the introduced nucleic acid can beidentified by drug selection (e.g., cells that have incorporated theselectable marker gene will survive, while the other cells die).

In certain embodiment, the amphiphilic molecules of the invention may beapplied to the interface in proteoliposomes which comprise more than onetype of protein or lipid. Therefore, the resulting ordered structure maycomprise one or more amphiphilic molecules (e.g., proteins, lipids,etc.).

For example, certain GPCRs involve a number of different membraneprotein. Therefore, it is advantageous to reconstituting these proteinsin proteoliposomes with more than one type of protein. Furthermore, italso may be advantageous to create ordered structures with more than onetype of protein or lipid in cases where signal transmitted by thereceptor is recognized and amplyfied by molecules other than thereceptor itself, (such as, but not limited to, the G protein), and wherethe signal is subsequently transmitted to an effector molecule (whichalso may be a membrane protein). Ordered structures containingmulti-protein and lipid systems may also be advantageous for othersignal transduction pathways where the transduction of signal isinitiated by hetero-dimer- or hetero-multimerization of differentprotein domains or protein species.

2. Two- and Three Dimensional Ordered Structures

The invention also pertains to two-dimensional ordered structures,comprised of a population of amphiphilic molecules. In a furtherembodiment, the two dimensional ordered structure comprises proteins,e.g., membrane proteins, cellular receptors, etc. In certainembodiments, the two dimensional ordered structures do not consistessentially of lipids. In a further embodiment, the two dimensionalordered structure of the invention is formed by planar membranecompression.

The term “planar membrane compression” is a method of forming orderedstructures comprising contacting a population of amphiphilic moleculeswith a interface, compressing said population to an appropriate pressurelaterally, such that a two-dimensional ordered structure is formed. In afurther embodiment, the method includes formation of a planar membranecomprising the population of amphiphilic molecules prior to formation ofthe ordered structure.

The invention also includes three-dimensional ordered structures (e.g.,“crystals”) of amphiphilic molecules formed by the methods of theinvention, e.g., contacting a population of amphiphilic molecules with ainterface, compressing said population to an appropriate pressure (e.g.,to or past the critical density), such that a three-dimensional orderedstructure is formed.

In a further embodiment, the two- and three-dimensional orderedstructures of the invention are suitable for structural determination ofthe amphiphilic molecule by diffraction techniques using electromagneticradiation or neutrons.

In a further embodiment, the two- and three-dimensional orderedstructures of the invention are mounted onto solid support.

The term “solid support” includes any support which allows for theordered structure to perform its intended function. For example, forscreening assays, the solid support may be selected such that it issuitable for manual or automated screening techniques. Examples of solidsupports which may be used include, but are not limited to, glass,plastic, wood, and other materials suitable for use in the art. Thesolid support may further have a reactive, hydrophobic, hydrophiliccoating. In other embodiments, the solid support may be a gel.

In certain embodiments, the solid support may be selected such that itis suitable for screening assays and other screening techniques. Exampleof screening assays include low, medium, high and ultra high-through putscreening assays.

3. Structural Determination Using Ordered Structures

Biological instruments are important tools for numerous applications inpharmaceutical, biotechnology, agriculture, food and home, personal careand cosmetics industry. The invention pertains, at least in part, tonovel technologies that can be used to study biological structure andfunction. For example, the methods and compositions of the invention maybe used to develop nanotechnology for multiple applications such as forearly stage drug discovery, target validation and lead optimization. Thetechnology may be comprised of a nanofabrication system, interfaced withadvanced optical analytical and micro diffraction techniques forfabrication of crystals and other ordered structures of amphiphilicmolecules, such as membrane protein systems. For example, the inventionpertains, at least in part, to protein chips (e.g., “NanoChip”) forapplications in screening assays, such as Structure-ActivityRelationship (SAR)-based High Throughput Screening (HTS) systems. Bycombining technologies, the invention should streamline drug selectionand lead identification processes for a wide range of membrane proteintargets.

Low-resolution structure information (comparable to that obtained froman electron diffraction projection data at around 10-25 Å) can beobtained by using the methods and ordered structures of the invention.For example, fluorescence imaging of the two-dimensional orderedstructures of amphiphilic molecules such as membrane proteins, formed atintermediate packing densities using planar membrane compression,provides information on the overall morphology of the protein moleculesin their native habitat.

Imaging the shape or molecular outline of a membrane protein isimportant to probing biological recognition events. For example,cytokine-driven interactions appear to be the initial event in signaltransduction for haemopoietin interferon receptors, receptor kinases,and the tumor necrosis factor (TNF)/nerve growth factor (NGF) receptors.In these systems, receptor multimerization allows information to passfrom the extracellular domain to the cytoplasmic environment without achange in the conformation of the receptor. In some receptors such asthose for epidermal growth factor (EGF) and platlet-derived growthfigure (PDGF), dimerization of the receptor leads to activation of theirintrinsic kinase activity. In yet another family, of receptors, e.g.,the G-protein coupled receptors, seven membrane spanning receptors, itis believed that the binding of the agonist to the receptor initiates achange in the conformation of the receptor that is recognized by theassociate G protein. In the signal transduction pathway, binding ofmolecular messengers (such as the human growth factors) to cellreceptors (such as tyrosine kinases TKO, initiates a series of complexevents that generally starts with a change in conformation ordimerization of the protein. Signal transduction is involved in diversecellular processes, including cell growth, reproduction, and migration.Any aberrations in these processes may result serious diseases such ascancer, diabetes, cardiovascular disease, and inflammation. In anembodiment, the invention pertains method for determining the shape ofan amphiphilic molecule. The method includes contacting a population ofthe molecule with a interface, compressing said population to anappropriate pressure, such that an ordered structure is formed, andanalyzing said ordered structure such that the shape of said amphiphilicmolecule is determined.

The term “shape” includes both the three dimensional structure of aparticular amphiphilic molecules in additional to the molecular outlineof a particular molecule. The term “molecular outline” refers to theoverall shape of the amphiphilic molecule in two dimensions such as thatobtained from an electron density imaging map of a protein crystal atlow resolution (5 Å or higher) and can identify alpha-helical regions asrods of electron density. The shape of the amphiphilic molecule can beused as a tool for rapid identification of a particular molecule or fordetermination of a change in conformation as well as hetero, homo, orother multimerization of particular species.

In one embodiment, the shape of said amphiphilic molecule is determinedby using electromagnetic radiation diffraction. Examples ofelectromagnetic radiation which may be used includes, but is not limitedto, light, electrons, x-rays, neutrons, or gamma rays. The shape of theamphiphilic molecule may also be determined by, for example, digitallaser fluorescence video microscopy, x-ray crystallography, or electroncrystallography. Advantageously, the shape of the amphiphilic moleculeis determined to a resolution of about 5 Å or higher.

In a further embodiment, the methods of the invention can be used todetect the effect of test conditions on particular amphiphilic moleculeby detecting shape changes of the molecule. In this method, the orderedstructure is subjected to test conditions and the shape of the moleculeis determined in the presence or absence of the conditions. In a furtherembodiment, the test conditions comprise contacting the amphiphilicmolecule with a test compound.

In an embodiment, the invention pertains to methods for providingdetailed structure information to near atomic resolution for amphiphilicmolecules, such as membrane proteins. This is one of the mostfascinating and challenging problems in structure-based (rational) drugdesign. If the protein is involved in either producing or preventing adisease state, information on its three-dimensional structure allows oneto affect that disease state. This can be done, for example, bydesigning small molecules which interact with specific sites on theprotein and alter its function or modulate its natural means ofoperation. The small molecules may inhibit, promote, antagonize,agonize, inverse agonize or otherwise alter the protein's activity.

The method includes obtaining an ordered structure comprising apopulation of amphiphilic molecules fabricated by the methods of theinvention, e.g., planar membrane compression, and determine thestructure of the amphiphilic molecules through electromagnetic radiationdiffraction techniques. High-resolution structural information can beobtained from protein ordered structures formed using electromagneticradiation diffraction techniques together with the methods of theinvention described herein for the formation of ordered structures.

In a further embodiment, the invention includes a method for determiningthe structure of a protein. The method comprises the steps of expressingsthe protein in a cell, obtaining said protein from the cell (e.g., byharvesting the membrane), applying the protein to an interface (e.g., ina crude or purified preparation, preferably without the use ofdetergents), compressing the protein on the interface to an appropriatepressure, such that an ordered structure of said protein is formed, andanalyzing the ordered structure (e.g., by electromagnetic radiationdiffraction or other techniques) such that the structure of the proteinis determined.

4. Screening Techniques Using Ordered Structures

In an embodiment, the invention pertains to a method for screening aordered structures for binding or other interactions with a testcompound. The method includes contacting the test compound with anordered structure; and analyzing the results of the interaction of thetest compound and the ordered structure, such that the test compound isscreened. In a further embodiment, the ordered structure is comprised ofprotein, e.g., a membrane protein. In another further embodiment, theordered structure is mounted on a solid support. Furthermore, theordered structures may be incorporated into protein chips as describedherein.

The term “screening” include both automated and manual techniques, andlow, medium, high and ultra-high throughput screening techniques. Theterm includes all methods used by those in the art of screeningincluding use of commercial plate readers, using imaging techniquesdescribed above as well as other binding assay including thermaltransition analysis and detection systems using an analog or digitaldetection mechanism of the electromagnetic radiation. Such mechanisms byexample include the eye(s) of the observer, CCD, photomultiplier tube,avalanche photodiode, etc. The test compounds may be screened forbinding, agonist, antagonist, inhibitor, or activator activity. The termscreening may refer to testing any number of test compounds oramphiphilic molecules desired. For example, the number of testcompounds, amphiphilic molecules, proteins, etc. may range from one togreater than a million.

Examples of test compounds which may be used in the methods of theinvention include small molecules, nucleic acids (e.g., RNA, DNA, etc.),carbohydrates, antibodies, and proteins. In certain embodiments,labeling the test compound may be advantageous. The test compounds ofthe present invention can be obtained using any of the numerousapproaches in combinatorial library methods known in the art, including:biological libraries; spatially addressable parallel solid phase orsolution phase libraries; synthetic library methods requiringdeconvolution; the ‘one-bead one-compound’ library method; and syntheticlibrary methods using affinity chromatography selection. The biologicallibrary approach is limited to peptide libraries, while the other fourapproaches are applicable to peptide, non-peptide oligomer or smallmolecule libraries of compounds (Lam, K. S. (1997) Anticancer Drug Des.12:145).

Examples of methods for the synthesis of molecular libraries can befound in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad.Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl. Acad. Sci. USA91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al.(1993) Science 261:1303; Carrell et al. (1994) Angew. Chem. Int. Ed.Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061;and in Gallop et al. (1994) J. Med. Chem. 37:1233.

Libraries of compounds may be presented in solution (e.g., Houghten(1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (LadnerU.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat. No. '409), plasmids(Cull et al. (1992) Proc Natl Acad Sci USA 89:1865-1869) or on phage(Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science249:404-406); (Cwirla et al. (1990) Proc. Natl. Acad. Sci.87:6378-6382); (Felici (1991) J. Mol. Biol. 222:301-310); (Ladnersupra.).

The term “small molecules” includes molecules such as peptides,peptidomimetics (e.g., peptoids), amino acids, amino acid analogs,polynucleotides, polynucleotide analogs, nucleosides, nucleosideanalogs, nucleotides, nucleotide analogs, organic (including, e.g.,heteroorganic and organometallic compounds) and inorganic compoundsincluding metals which may bind to the protein or amphiphilic molecule.The term “small molecule” includes compounds which have a molecularweight of about, for example, 10,000 grams per mole or less, 5,000 gramsper mole or less, 2,000 grams per mole or less, or 1,000 g/mol grams permole or less. In a further embodiment, the small molecule is an organiccompound. Organic compounds comprise one or more carbon atoms. Inanother embodiment, the compound is an inorganic compound. Inorganiccompounds include compounds which do not comprise a carbon atom.

The invention provides a method (also referred to herein as a “screeningassay”) for identifying modulators, i.e., test compounds or agents(e.g., peptides, peptidomimetics, small molecules or other drugs) whichbind to the amphiphilic molecules of the ordered structures of theinvention which have a stimulatory or inhibitory effect on, for example,the amphiphilic molecule's activity.

In one embodiment, the invention provides assays for screening candidateor test compounds which are substrates of an amphiphilic molecule. Inanother embodiment, the invention provides assays for screeningcandidate or test compounds which bind to or modulate the activity of anamphiphilic molecule.

The ability of the test compound to modulate the binding of anamphiphilic molecule to a substrate can be determined. Determining theability of the test compound to modulate the binding of an amphiphilicmolecule to a substrate can be accomplished, for example, by couplingthe amphiphilic molecule's substrate with a radioisotope or enzymaticlabel such that binding of the amphiphilic molecule's substrate to theamphiphilic molecule can be determined by detecting the labeledamphiphilic molecule's substrate in a complex. Alternatively, theamphiphilic molecule could be coupled with a radioisotope or enzymaticlabel to monitor the ability of a test compound to modulate theamphiphilic molecule's binding to a substrate in a complex. Determiningthe ability of the test compound to bind an amphiphilic molecule can beaccomplished, for example, by coupling the compound with a radioisotopeor enzymatic label such that binding of the compound to the amphiphilicmolecule can be determined by detecting the labeled amphiphilic moleculecompound in a complex. For example, compounds (e.g., the amphiphilicmolecule's substrates) can be labeled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, eitherdirectly or indirectly, and the radioisotope detected by direct countingof radioemmission or by scintillation counting. Alternatively, compoundscan be enzymatically labeled with, for example, horseradish peroxidase,alkaline phosphatase, or luciferase, and the enzymatic label detected bydetermination of conversion of an appropriate substrate to product.

In an embodiment, an assay of the present invention comprises contactingan amphiphilic molecule with a test compound, such that the ability ofthe test compound to bind to the amphiphilic molecule is determined.Binding of the test compound to the amphiphilic molecule can bedetermined either directly or indirectly. In an embodiment, the assayincludes contacting the amphiphilic molecule with a known compound whichbinds the amphiphilic molecule to form an assay mixture, contacting theassay mixture with a test compound, and determining the ability of thetest compound to interact with an amphiphilic molecule, whereindetermining the ability of the test compound to interact with anamphiphilic molecule comprises determining the ability of the testcompound to preferentially bind to an amphiphilic molecule as comparedto the known compound.

In another embodiment, a test compound is contacted with an orderedstructure and the ability of the test compound to modulate (e.g.,stimulate or inhibit) the activity of the amphiphilic molecule of theordered structure is determined. Determining the ability of the testcompound to modulate the activity of an amphiphilic molecule can beaccomplished, for example, by determining the ability of the amphiphilicmolecule to bind to a target molecule. Determining the ability of theamphiphilic molecule to bind to a target molecule can be accomplishedusing a technology such as the methods of the invention.

In yet another embodiment, the assay involves contacting an amphiphilicmolecule with a known compound which binds the amphiphilic molecule toform an assay mixture, contacting the assay mixture with a testcompound, and determining the ability of the test compound to interactwith the amphiphilic molecule, wherein determining the ability of thetest compound to interact with the amphiphilic molecule comprisesdetermining the ability of the amphiphilic molecule to preferentiallybind to or modulate the activity of the known compound.

The analysis of the interaction of the test compound and the orderedstructure may comprise analyzing the shape changes of the protein. Shapechanges include conformational changes (e.g., folding, unfolding),multimerization (e.g., dimerization, trimerization, etc.),fragmentation, and other changes which can be detected using the methodsof the invention.

For example, in an embodiment, the interaction between the protein and atest compound can be monitored using high-performance CCD or otherdigital or analog imaging techniques and/or by capturing the photonusing the eyes, a CCD, a photodiode, or a photomultiplier tube. Sonveauxet al. reported a change in the tertiary structure of reconstituted P-gpboth in the presence and in the absence of MgATP, and MgATP-verapamil(J. Biol. Chem. 271, 24617-24 (1996)). In the methods of the invention,the change in the shape of the P-gp would be monitored, for example, byfluorescence imaging of the domains, using a fluorescent analog ofverapamil (Molecular Probes) in the presence and absence of MgATP.

In a further embodiment, the interaction of the amphiphilic molecule,such as a protein (e.g., a receptor) with the test compound can bemonitored using thermal microanalysis, whereby binding of the testcompound to the receptor is monitored through depicting a change in thethermal transition of the receptor in the presence and absence of thetest compound using microcalorimetry.

The methods of the invention take advantage of the quantitative imagingcapability of advanced imaging as well as photon counting techniquessuch as high-performance CCDs, to demonstrate simple binding assays todepict high-affinity binding of a ligand such as verapamil to P-gp. Avariety of different illumination techniques may be used to measureequilibrium binding of a test compound to the protein., for example, twosuch techniques include (1) incident light (epi-) illumination may beused to monitor interactions of high binding affinity ligands. TotalInternal Reflection Fluorescence (TIRF) using a block preferably withcylindrical symmetry may be integrated with the imaging system to probeequilibrium binding affinity of low-affinity binding ligands directly atequilibrium and without perturbing the equilibrium (Mojtabai, F., Ph.D.Thesis pp. 1-129 (University of Basel, Switzerland, 1985). Superiorcharacteristics of TIRF vs. incident-light illumination have beendiscussed in detail elsewhere. Briefly these include a low depth ofpenetration of light to allow optical sectioning to 20 nm in the zdirection. This low depth of penetration reduces background illuminationfrom out of focus planes in the solution. This significantly enhancesthe sensitivity of binding assays. These fluorescence illumination byepi-fluorescence or TIRF may be combined with Fluorescence RecoveryAfter Photobleaching or Polarized Fluorescence Recovery AfterPhotobleaching to measure binding kinetics and degree of aggregation.

The methods of the invention also may be used for identifying particularproteins of interest in tissue samples (e.g., blood, muscle, fat, hair,cells, etc.), by obtaining a sample of a cell, applying the sample tothe interface, compressing the sample on said interface to anappropriate pressure, such that an ordered structure is formed; andidentifying the protein of interest in the ordered structure. Preferablythe sample of a cell is a membrane preparation, e.g., a crude membranepreparation. In one further embodiment, the identification methodinvolves contacting the ordered structure of the invention with an agentwhich binds to the ampiphilic molecule of interest. Agents which bind toproteins and can be detected are known in the art. Examples of agentswhich can bind to proteins include antibodies.

Furthermore, the assay methods of the invention may further comprise theuse of ordered structures which are comprised of more than one type ofamphiphilic molecule in the ordered structure. These ordered structurescan be synthesized by applying multicomponent proteoliposomes to aninterface and compressing it to an appropriate pressure to yield anordered structure of the invention.

In an embodiment, these multicomponent proteoliposomes may include amixture of amphiphilic materials such as, but not limited to,phospholipids, cholesterol and the membrane protein beta amyloidprecursor protein (APP). The resulting ordered structures of membranepreparations may be used to develop an assay to determine how loweringcholesterol might inhibit clipping of the APP by certain enzymes toprevent formation of the neurotoxic peptide beta-amyloid and tosubsequently inhibit the formation of plaques in the Alzheimer'sdisease. In a recent article, new research suggests thatcholesterol-lowering treatments inhibit formation of beta-amyloid byshifting the balance of activities of enzymes that clip the APP (such asthe beta-, and gamma-secretase) to produce the neutrotoxin, to favorthose enzymes (such as the alpha-secretase) that prevent the productionof the neurotoxic peptide (Science Vol. 294, Pages 508-509). It has thusbeen deduced that beta-, and gamma-secretase may have greater access toclip APP in cholesterol rich cell membrane rafts than in phospholipidrich areas of the cell membrane. Such analysis may lead to developmentof new diagnostics and therapeutic systems that can be used to detectand cure the Alzheimer's disease.

5. Protein Chips and Other Ordered Structures Products

As DNA-based biochip technology continues to find applications in DNAanalysis, the protein chips (e.g., protein “Nanochips”) of the presentinvention may also be used in numerous applications. In one embodiment,the invention pertains, at least in part to a protein chip, whichincludes a solid support and at least one ordered structure of apopulation of amphiphilic molecules. The ordered structures of theprotein chip may be either two or three dimensional. The protein chipmay also further comprise additional ordered structures of the same ordifferent amphiphilic molecules. The protein chip may comprise orderedstructures of any number of amphiphilic molecules, preferably with eachdifferent amphiphilic molecule contained in discrete wells. The numberof ordered structures of amphiphilic molecules may range from one totens of thousands or more. In other embodiments, ordered structures ofthe same amphiphilic molecule is present in each of the wells of theprotein chip. In certain embodiments, the amphiphilic molecules of theprotein chip are proteins and, in yet a further embodiment, may bemembrane proteins. Preferably, the protein chip is suitable forscreening methods, e.g., automated screening techniques such as low,medium, high and ultra-high through put screening techniques.

The methods of the invention will be used to create protein chips (e.g.,“NanoChip”). The basic design of the protein chip will have flexibilityto be suitable for use in screening assays, such as, but not limited to,High Throughput Screening (HTS) systems. Alternatively, the inventionalso pertains, at least in part, to a stand-alone SAR-based UltraHigh-Throughput Screening (UHTS) system, by integrating the protein chip(e.g., “NanoChip”) with highly sensitive optical detection systems andadvanced micro-robotics technologies. The protein chips of the inventionare expected to meet the market needs for automation, highersensitivity, accuracy and precision as well as increased samplethroughput and decreased unit cost. Other applications of the protein(“NanoChip”) are in developing analytical devices to probe molecularrecognition events, or alternatively, it can be incorporated intodiagnostic imaging devices.

The protein chip can be used for a wide-range of applications indifferent areas; such as receptor-ligand interactions, competitivebinding analysis, monitoring ligand-induced conformational changes,protein structure analysis, immunoassays, enzyme-substrate interactions,protein quantification, trace protein detection, protein-DNAinteractions, as well as monitoring gene expression. Other areas includeprobing the signal transduction events, and developing diagnosticsimaging devices, for example to assay Multidrug Resistance.

Preferably, the protein chip of the invention comprises a plurality ofordered structures in discrete wells. The number of wells can be anynumber which allow the protein chip to perform its intended function.For example, a protein chip may comprise numerous wells with the sameprotein in ordered structures in each discrete well, or differentproteins in ordered structures in each discrete well. In yet anotherembodiment, the invention also includes compatible components for futureuse in commercial fluorimetric microplate readers or imagers.

In a further embodiment, the protein chip comprises discrete orderedstructures in a multiwell array (e.g., high density multiwell array), ona solid substrate, preferably formed of a transparent, rigid substance,such as fused silica. The two-dimensional or three-dimensional orderedstructures of proteins may be extended from a single-well (for example,the glass bottom of a trough as described in U.S. Pat. No. 5,044,308) toa multi-well array. A schematic drawing of a protein chip of theinvention is shown in FIGS. 1 a and 1 b. FIG. 1 a is a top view of theplate 100 of the trough 10 including a plurality of micro-wells 101 forfabricating an array of ordered structures of membrane proteins. FIG. 1b is a cross-sectional view of the plate 100 illustrated in FIG. 1 a. Asshown, the arrays are formed on a glass substrate 102 or a substrateformed of another suitable material. The microwells are formed byfabricating raised polymer walls 103 on the substrate. Preferably, thepolymeric compound is a hydrophobic inert material, such as afluoroelastomeric material, e.g., Teflon (DuPont),and are between aboutten and about twenty microns thick. Briefly, a negative mask isfabricated using a thin, flat piece of metal or plastic, to denote theraised rims of each well 101. The mask is placed on the glass substrate102 of the trough. A thin film, preferably between about ten and abouttwenty microns, of liquid Teflon (DuPont) is sprayed or deposited on theglass substrate 102 in order to cover the unmasked regions. To ensurebetter adhesion of Teflon to glass, the unmasked regions may bepre-etched prior to the deposition process. Different sizes and shapesof micro-wells can be fabricated on the glass substrate by usingdifferent mask geometry. The solvent will be allowed to evaporate byapplication of heat or drying under a stream of nitrogen to preventcontamination of the substrate with impurities.

After formation of the wells, the glass substrate is mounted at thebottom of the trough. Ordered structures are fabricated as describedearlier. The ordered structures are transferred to the protein chip, bya horizontal deposition, namely by lowering the depth of water in thetrough until the height of the film of water reaches the height of theraised walls of the trough. Further lowering of the depth of water willcause a separation between the contents of each well as the film ofwater breaks at the raised heights surrounding the well. Alternatively,the ordered structures may be transferred to a different solid support(e.g., another chip), at a gas/solid, liquid/solid, or solid/solidinterface. The microstructure may be cryo-preserved for electronmicroscopy and diffraction analysis or for purposes of preservationuntil future use. The transfer process may be made manually or remotelyby using a robotic arm. The solid support may constitute a chemicallyinert, hydrophobic or hydrophilic material coated or uncoated withfunctionally active or inactive compounds. Such materials include, forexample, glass, quartz, metals, metal oxides, silicon oxide, teflon,plastics, and mica. Each material may be coated with a layer of othermaterials such as graphite or silica oxide or gels includingfunctionally active compounds to capture the ordered structures. Thecontents of each well can then be analyzed independent from othersurrounding wells. The fidelity of the transfer of the orderedstructures to the chip will be assessed, by fluorescence microscopicmonitoring of the shape of the protein ordered structures.Alternatively, one can measure binding of a test compound to the proteinin a quantitative or qualitative SAR-based HTS screening mechanism usingan analog or digital detection technique such as a CCD, photomultiplier,or avalanche photodiode. Future commercial production costs should below due to the availability of robust microfabrication procedures suchas aqueous-based etch procedures, and photoresists for precisepatterning the wells (Burns, M. A., et al. Science 282, 484-487 (1998)).

The protein-chip, (e.g., “NanoChip”), together with such advancedsurface-selective illumination techniques constitutes the basiccomponents of an integrated turn-key high throughput screening system.Alternatively, the protein chip may be used in existing commercialmicroplate readers or other imaging devices.

Applications of protein chips, include, for example, an integratedSAR-based HTS or a functional group imaging system in combination with ananotip AFM or by using Surface Plasmon Polaritons. Chemically modifiednanotube tips, that are now available for atomic force microscopy (AFM)of biological specimen, can be used for functional group imaging of theordered structures (Wong, S. S. et al. Nature 394, 52-55 (1998)). Inaddition, the nanotip AFM can be used in combination with fluorescenceimaging of the ordered structures to provide a topographicthree-dimensional view of the amphiphilic molecule's molecular outline.

The ordered structures of amphiphilic molecules can be attached orotherwise associated with a solid support to facilitate screeningassays. Binding of a test compound to an amphiphilic molecule of anordered structure, or interaction of an amphiphilic molecule of anordered structure with a target molecule in the presence and absence ofa test compound, can be accomplished in any vessel suitable forcontaining the reactants. Examples of such vessels include microtiterplates, such as the protein chips of the invention. For example, theprotein chips may be combined with the test compound, and the mixtureincubated under conditions conducive to complex formation (e.g., atphysiological conditions for salt and pH). Following incubation, theprotein chip wells are washed to remove any unbound components, complexdetermined either directly or indirectly, for example, as describedbelow.

6. Apparatus and Instrumentation for Formation and Analysis of OrderedStructures

Special instrumentation may be useful if this process is to be used indiverse disciplines for a wide range of applications. Specifically,fabrication of ordered structures by compression a planar membranebeyond a critical density point (over-compression) barriers that areresistant to film leakage at high surface pressures may be advantageous.Advantageously, the instrument also should provide for: (i) controlledfabrication of uniform micro- and nanostructures, (ii) monitoring theformation of the structures by real-time fluorescence imaging, and (iii)transferring the micro- and nanostructures to a solid support for atomicscale measurements.

In an embodiment, the invention pertains to a system for controlledfabrication of ordered structures of amphiphilic materials, e.g.,membrane proteins. The system may be integrated with advanced surfaceselective fluorescence and non-fluorescence imaging systems, as well asa robotic mechanism to transfer the fabricated ordered structures to asolid support for preparation of specimen and a device to subsequentlyflash freeze the proteins in the ordered structures at cryogenictemperatures.

The illustrative embodiment of the invention provides an integratedtrough system for forming and analyzing an ordered structure on asubphase in an efficient and controlled manner. According to theillustrative embodiment, the system of the present invention includes atrough for the forming an ordered structure by compression of apopulation of amphiphilic molecules. The trough includes a barrier forcompressing the population that is resistant to leakage at high surfacepressures. A suitable trough is described, for example, in U.S. Pat. No.5,044,308, the contents of which are herein incorporated by reference.The integrated trough system includes an image acquisition andprocessing system integrated with the trough for acquiring, processing,storing and printing images of the ordered structure formed by thetrough. The integrated system further includes a temperature regulatedhousing for maintaining a precise temperature during formation of theordered structure, and an automated ordered structure transfer systemfor transferring an ordered structure formed in the trough to acryochamber. The integrated trough system of the illustrative embodimentallows for controlled fabrication of uniform ordered structures,monitoring of the formation of the ordered structures in real-time andtransferring of the ordered structures to a solid support for atomicscale measurements.

Briefly, the trough used in the illustrative embodiment of the inventionand described in U.S. Pat. No. 5,044,308 is used to fabricate orderedstructures at air-aqueous interfaces via planar member compression andcomprises a frame having top and bottom separable frame portions. Aplate is disposed within the frame for holding a subphase. The plate ispreferably formed of a transparent rigid substance, such as fused silicato allow imaging through the plate of a structure formed thereon. Asealing element of chemically inert material is positioned between thetop of the plate and the top frame portion and preferably comprises aperfluoroelastomeric material that is conformable to the top of theplate and to the top frame portion to prevent subphase leakage from thetrough. A movable barrier is provided for laterally compressing apopulation of amphipilic molecules deposited on the subphase to form anordered structure. An additional sealing element of chemically inertmaterial may be spaced adjacent to the above-mentioned sealing element,and also positioned between the top of the plate and the top frameportion for cooperating with the above-mentioned sealing element toprevent the subphase from reaching the frame. One skilled in the artwill recognize that the present invention is not limited to the troughdescribed in U.S. Pat. No. 5,044,308, and that any suitable structurefor forming an ordered structure by compression may be utilized.

An advantage of the trough described in the '308 patent is that theconfiguration of the trough allows for a lower depth of water in theplate, typically less than 0.5 mm. The reduced water depth reducesconventional flow transferred from the aqueous subphase to the orderedstructure, thereby permitting direct fluorescence microscopicobservation of distinct features in the ordered structure withoutrequiring the use of flow retardation devices commonly used in othermicroscope troughs, which limit the observation area and perturbs theordered structure.

According to the illustrative embodiment, shown in FIG. 2, the trough 10is integrated with an image acquisition and processing system 50 toallow for in-situ characterization of the structure formation throughoutthe fabrication process. In the illustrative embodiment, the imaging andimage processing system is a real-time digital laser-fluorescence videomicroscopy system including an inverted fluourescence microscope 51,such as an Olympus IMT-2 equipped with epi-illumination optics forviewing the trough 10. The microscope 51 is connected to a video camera52 for generating, storing and displaying analog video signalsrepresentative of the ordered structure viewed by the microscope. Thevideo camera is connected to a monitor 62 for displaying the video imageand processor 53, including an imaging board 54 for storing still framedigital images of the ordered structure formed in the trough. Theimaging board is connected to a second monitor 69 for displaying thedigital images of the ordered structure. The illustrative imageacquisition and processing system further includes color ink jet printer55 for printing color images and a laser printer 56 for printing blackand white images. A data switch 57 directs a data signal representativeof an image of the ordered structure to a selected printer. The systemfurther includes a scanner system 58 for scanning transparencies andnegatives and storage devices for storing the digital images. Oneskilled in the art will recognize that the invention is not limited tothe illustrative image acquisition and processing system, and that anysuitable arrangement for acquiring, storing, viewing, processing and/orprinting images of the structure formation may be utilized.

The illustrative trough 10 is mounted on the stage of the invertedfluorescence microscope 51 to allow visualization of an orderedstructure formed in the trough. A light source, such as a laser or alamp, excites selected fluorescent probes within the ordered structure.According to the illustrative embodiment, an air-cooled argon laser isused to excite fluorescence emission with either a 488 or 514 nanometerline. The microscope of the illustrative embodiment is equipped with twodifferent sets of filters for emission of FITC, as well asrhodamine-type fluorescence. The fluorescein filters of the illstrativeembodiment include a 505-nm dichroic long pass filter and a 515-nm longpass emitter, from Chroma Technology Corporation. The rhodamine filtersmay comprise a 565 nm dichroic long pass filter and a 580-nm long passemitter. After the light source excites the ordered structure in thetrough 10, the emitted fluorescence from the ordered structure isobserved through the microscope objective. In order to observe theordered structure, a small amount, between about 1-2 mole %, of afluorescent amphiphilic dye is mixed with the population of amphiphilicmolecules. A high power, high numerical aperture objective with highcollection efficiency can be utilized, due to the low depth of water inthe trough. The illustrative configuration allows imaging by opticalsectioning throughout the shallow aqueous subphase, which isaccomplished by zooming the objective at different heights through thetransparent plate at the bottom of the trough. In this manner, theintegrated system permits tracking of the formation of microstructuresthroughout the entire working volume of the trough, e.g. at theair-water interface, throughout the shallow aqueous subphase, as well asthe liquid solid interface at the bottom of the trough.

According to the illustrative embodiment, the video camera 52 is a SonyDXC-9000 color video camera attached to the microscope 51 via a videocoupler 60, though one skilled in the art will recognize that anysuitable electronic device for recording images of an object may beutilized. The imaging device of the video camera of the illustrativeembodiment incorporates three ½ inch progressive scan CCD chips. Thedynamic resolution of the images is 700×480 TV lines. A video recorder61, such as a Sony Videocassette Recorder model SV009500MD, records ananalog video signal representative of an image captured by themicroscope in real-time. A color monitor 62, such as a 13-inch PVM-14N2USony color video monitor with 500 TV line resolution, in communicationwith the video camera 52, displays the video signal generated by thevideo camera.

According to the illustrative embodiment the imaging board 54 is aFlashPoint-128™ high performance high resolution video capture boardfrom Integral Technologies with a 4 Mb MDRAM and SuperVGA Windowapplication. The processor 53 containing the board 54 comprises aPentium II 300 Mhz in a model G6-300 personal computer 67 from Gatewayhaving a 4GB SCSI hard drive, 128 MB RAM running under a Windowoperating system. The analog outputs of the imaging board 54 areconnected to the appropriate inputs of the computer monitor 69,illustrated as a 19-inch EV900 color CRT from Gateway with a 1600×1200maximum resolution and 0.26 pitch. One skilled in the art will recognizethat any suitable imaging board and processor may be utilized to processand store still frame digital images of the ordered structure formed inthe trough, in accordance with the teachings of the invention.

According to the illustrative embodiment, images of the orderedstructure are acquired and processed using ImagePro Plus 3.0 softwarefor Windows 95 from Media Cybernetic, and dynamic time-lapse orreal-time representations are made using the ImagePro Plus Sequencerfunction, allowing a user to view a sequence of stored image files at acontrolled speed. A storage device, such as a 650 Mb Hitachi CD-R 64, anIomega 1 Gb Jaz 65, a 100 Mb Zip drive 66 or any other suitable storagedevice may be utilized to archive the digital data. Digital images canbe processed for color contrast and brightness enhancement using theAdobe PhotoShop 4.0 or any other suitable processing software. Accordingto the illustrative embodiment, the color printer 55 comprises an EpsonStylus Color 800 Ink Jet output device with up to 1440×720 dpiresolution using Epson Photo Quality Ink Jet paper at 720 dpi. The blackand white laser printer 56 of the illustrative embodiment comprises anHP LaserJet 6P/6MP printer with 600 dpi resolution. The scanner 58 ofthe illustrative embodiment comprises a Microtek ScanMaker III 36-bitflatbed scanner with 600×1200 dpi optical resolution (96,000 dpiinterpolated). The scanner 58 includes a Transparent Media Adapter toallow scanning transparencies and negatives. One skilled in the art willrecognize that the invention is not limited to the illustrativeembodiment and that variations may be made without departing from thescope of the invention. For example, the image acquisition andprocessing system is not limited to the described printers, scanner,storage devices and software and any suitable product may be utilized.

According to one embodiment, shown in FIGS. 3 a and 3 b, the trough 10is utilized with a temperature regulated housing system 70 foraccurately controlling the operating temperature within the troughenvironment during formation of the ordered structure. The illustrativetemperature control system 70 provides precise temperature regulationwithin a −10 to +40° Celsius range to within +−−0.1° Celsius of aselected reference temperature. The illustrative temperature regulatedhousing comprises a proportional-integral feedback control system,illustrated in the block diagram of FIG. 2 a. The control systemincludes a temperature sensor 71 for measuring the temperature of thesubphase in the trough 10 and a temperature actuator 73 for adjustingthe temperature within the trough 10. The temperature control systemfurther comprises a controller 72 for controlling the actuator 73 inresponse to the actual temperature measured by the sensor 71. Thecontroller 72 inputs are the actual temperature signal measured by thetemperature sensor and a selected reference temperature signal, set by auser. The controller 72 compares the actual temperature to a desiredtemperature and triggers the actuator 72 to adjust the actualtemperature by a selected amount to equal the desired temperature.

As shown in FIG. 3 b, the temperature control system 70 controls thetemperature within an enclosed volume defined by a housing 74 enclosingthe trough 10. According to the illustrative embodiment, the housing 74is formed of 0.5 mm thick plexiglass, though one skilled in the art willrecognize that alternate materials may be utilized. The illustrativehousing 74 encloses a volume of less than about 51 liters around thetrough 10. The housing includes a plurality of sealable openings 75, 76,77 to facilitate access to the trough. The openings 75, 76, 77 aresealed from the outside by sliding doors formed of plexiglass. An innertrough cover 78, also preferably formed of plexiglass, directly coversthe trough 10, which is mounted onto the microscope stage 79 via amicroscope trough adapter 80. The temperature controlled housing system70 further includes a microscope stage adapter 81 for mounting thehousing 74 to the microscope stage 79.

The integrated system further includes an automated ordered structuretransfer device 82, comprising a robotic arm, for transferring anordered structure formed in the trough 10 according to the teachings ofthe present invention to a solid support 86 for further atomic scaleexamination. The solid support may comprise a small solid support, suchas an electron microscope grid or large solid support, such as amicroscope cover glass or an oxidized silicon support. The orderedstructure transfer device 82 accesses the trough 10 through the one ofthe openings 75, 76, 77 in the housing 74. A number of analyticaltechniques can be employed to the supported ordered structure in orderto characterize its structure to subnanometer resolution. Thesetechniques include high-resolution electron microscopy,electron-diffraction, synchrotron micro-focus x-ray diffraction, as wellas scanning probe microscopies, such as atomic force microscopy (AFM) ornear-field scanning optical microscopy (NSOM). Molecular recognitionevents and low resolution structural analysis of the protein can befurther studied at either an air-aqueous interface or at a solid supportusing a number of advanced surface-selective techniques, including TotalInternal Reflection Fluorescence (TIRF) and Fluorescence Recovery AfterPhotobleaching (FRAP), with polarized or non-polarized illumination,Surface Plasmon Polaritons (SPP), and Scanning Probe Microscopies, suchas AFM. The illustrated system further comprises a cryochamber 85 forpreserving a specimen formed in the trough at cryogenic temperatures ina frozen hydrated state for further analysis.

The temperature actuator 73 of the illustrative embodiment comprises apair of thermoelectric cooling devices (TEC) mounted diagonally belowthe microscope stage adapter 81. The thermoelectric cooling devices 73produce a temperature differential to increase or decrease thetemperature in the trough 10. A thermoelectric cooling device is aspecial type of semiconductor that functions as a heat pump. By applyinga low-voltage, high-current, DC power source, heat will be moved in thedirection of the current. The heat is pumped from one side of thethermoelectric cooling device to the other, so that one face will becold while the opposite face will be heated, and the effect isreversible. One skilled in the art will recognize that any suitabledevice for heating or cooling the trough subphase and/or troughenvironment may be utilized. The illustrative temperature sensor 71 formeasuring the temperature of the subphase in the trough comprises aK-type thermocouple model KMTSS-0100G-6, with a probe diameter of 0.010″and SMP-K-M connector, though one skilled in the art will recognize thatany suitable temperature sensor may be utilized. The thermoelectriccooling device applies the temperature differential to the trough via analuminum plate in the bottom of the housing 74, which cools the aqueoussubphase in the trough by convection of heat. According to theillustrative embodiment, the maximum heat pump of the thermoelectriccooling devices 73 is 127 watts, operating at 14 amps, capable ofproducing a “no load” temperature differential of approximately 67° C. Apair of liquid heat exchangers 83 located below the thermoelectriccooling devices form heat sinks for absorbing the heat produced on thehot side of the thermoelectric modules during a cooling cycle. Theliquid heat exchangers 83 are cooled by water at about 0° C. Aperistaltic pump 84 is provided to move water through liquid-sealedpipes in the heat exchanger at a rate of about 10 ml/s. One skilled inthe art will recognize that any suitable device for providing a heatsink may be utilized.

FIGS. 4 a and 4 b are schematic diagrams of the electronic temperaturecontrol design system for controlling the temperature of the subphaseaccording to the illustrative embodiment. The output of the temperaturesensor 71, corresponding to the temperature in the subphase, isintegrated via a closed loop circuit to a proportional-integral (PI)controller board 72 designed to be used with a thermoelectric coolingdevice or other suitable cooling device or heat pump. As shown in FIG. 4a, a conductor-shielded cable 96 provides an electrical connectionbetween the temperature sensor 71 and the controller board 72. Thecontroller board 72, shown in detail in FIG. 4 b, controls the input tothe thermoelectric cooling device 73, which accordingly determines thetemperature in the trough.

According to the illustrative embodiment, the controller board 72 is aSeries P-1 Thermoelectric Cooler controller board from Alpha OmegaInstruments Corp. The controller 72 features a metal oxide semiconductorfield-effect transistor 91 (MOSFET) or other suitable power amplifier,together with proportional and integral (PI) temperature control. Theillustrative controller board 72 is powered by a DC power source 92. Theillustrative controller board comprises an input/output system, such asa twenty-pin Molex connector 97, for attaching the temperature controlsystem to a temperature control interface board. The connector 97includes input control lines for the connecting the power supply 92 tothe connector 97, the current temperature input 93, transmitted from thethermocouple 71, a reference temperature set point 94 for setting thedesired temperature of the subphase and a maximum current set point 95.According to the illustrative embodiment, the temperature set point andmaximum set point are adjusted by the user using single-turn adjustmentpotentiometers. As illustrated, the MOFSET 91 is located between the TEC73 and a TEC power supply 98. The controller board 72 further includes acurrent sense resistor 88, illustrated as two 0.1 ohm resistors inparallel, connected to ground and a double-pole, double-throw (DPDT)relay 89. Relays are electromagnetic switches that can turn a largeamount of current on or off by using a relatively small amount ofcurrent. The relay 89 allows the controller 72 to operate in unipolar(i.e. providing heating or cooling) or bipolar (i.e. providing heatingand cooling) mode. One skilled in the art will recognize that anysuitable switch for allowing bipolar operation may be utilized accordingto the teachings of the invention.

To control the temperature in the trough, the temperature sensor 71measures the current temperature in the trough and transmits a currenttemperature signal indicative of the temperature in the subphase of thetrough 10 to the controller 72. The controller 72 compares the currenttemperature with the desired temperature, set by the user at referencetemperature set point 94, and generates an error signal if the currenttemperature deviates from the desired temperature. The error signaltriggers the actuator 73, i.e. the thermoelectric cooling devices, toequalize the two temperatures by increasing or decreasing thetemperature in the trough by a predetermined amount.

The illustrative temperature control system provides efficient andaccurate temperature control for the formation process without incurringhigh costs. The illustrative design allows the use of high capacitythermoelectric cooling devices to efficiently control the temperature ofthe trough. The illustrative design is also less expensive than currentcommercial models and allows for relatively easy implementation offuture upgrades.

The integrated system of the illustrative embodiment further includes anenhanced software system allowing for the simultaneous execution ofseveral tasks, including control of the ordered structure, temperaturecontrol and image acquisition. FIG. 5 is a block diagram of the softwaremodules forming the enhanced software system of the illustrativeembodiment. FIG. 5 further illustrates the data flow path between themain control application program 111 and various software modules, whichstore instructions for performing particular tasks in dynamically linkedlibraries (DLL). To perform a particular task, the main controlapplication program 111 calls the DLL in a respective linked card andexecutes the instructions stored therein. The image acquisition softwareis a three-dimensional imaging system allowing a user to gathertwo-dimensional data sets at different time points during apressure-area experiment. The software system 110 includes a maincontrol application 111, a temperature controller card 112 forinterfacing with the temperature control system described above and avideo frame grabber card 115 interfacing with the video camera 52 forcontrolling video acquisition and image processing. Video frame grabbingrefers to the step of converting analog video signals of an object todigital signals that a computer can process. The video frame grabbercard 115 provides instructions for digitizing images of the orderedstructure in the trough in real time and storing the images in thememory of the imaging board 54. The software system 110 further includesan LVDT interface card 113 and a microprocessor-based motion controllercard 114, such as a motor controller card from Galil Motion Control,Inc. for controlling movement of the microscope 51 and/or the automatedordered structure transfer device 82 with respect to the trough 10.

FIG. 6 illustrates a graphical user interface 120 generated by thesoftware system of the present invention. As shown, the enhancedsoftware allows ordered structure parameters, as well as an image of theordered structure to be displayed simultaneously. The image acquisitionsoftware of the illustrative embodiment is a three-dimensional (3-D)imaging system. This allows the user to gather two-dimensional data setsat different time points during a pressure-area experiment, e.g., duringthe formation of an ordered structure. The three-dimensional imagingsoftware utilizes the Image-Pro Plus (from Media Cybernetic) imageanalysis software for acquiring and analyzing images of the orderedstructure formed in the trough 10, though one skilled in the art willrecognize that any suitable image processing software may be utilized.This software provides an application programmer's interface for remotecontrol of the video frame grabber function from within the softwaresystem. The ordered structure's physical parameters as well as imagedata may be viewed simultaneously through the graphical user interfacedisplayed on the PC monitor. Each image is time-stamped and stored alongwith the ordered structure's physical parameters. As illustrated in FIG.6, the ordered structure parameters are displayed in a first applicationwindow 121, whereas the image of the ordered structure, captured by theimage acquisition and processing system of the illustrative embodiment,is displayed in a second application window 122. According to analternate embodiment, video images recorded by the video recorder areincorporated directly into the first application window 121 anddisplayed.

The imaging software allows the user to configure and control the imageacquisition conditions. Upon starting an experiment, live capture fromthe microscope's video camera is enabled. The user is prompted to setthe desired video image capture interval. The user is permitted toprovide custom interval settings or to use the software's defaultsettings. At this point the user can choose between a static time-delaybetween acquisitions (for example, sampling every minute), a variabletime delay, or alternatively a manual time delay (capture on demand).The amount of RAM and the size of the hard drive installed in thecomputer system 67 determine the total number of images captured duringan experiment.

In an embodiment, the invention pertains to a method of forming orderedstructures of amphiphilic molecules (e.g., proteins), by applyingamphiphilic molecules to a subphase (e.g., an gas-aqueous interface,e.g., an air-water interface) and compressing them to an appropriatepressure, such that ordered structures (e.g., crystals and other nano-or micrometer scale ordered arrays) with desired dimensions andcharacteristics are formed. The technique is simple and versatile foruse with most amphiphilic molecules that can be spread at a subphase(e.g., an air-water interface). The technique entails molecularengineering based upon compressing a population of amphiphilic moleculeson an interface to an appropriate pressure. Briefly, a population ofamphiphilic molecules is applied to a subphase (e.g., at an air-aqueousinterface of the monolayer trough). The planar membrane may becompressed by means of a barrier. Further compression of the planarmembrane, e.g., monolayer, toward or beyond its critical point (e.g.,their limiting area/molecule), result in the formation of two- and/orthree-dimensional mono- or multilayered ordered structures that may besimilar to crystal structures observed in bulk.

Amphiphilic molecules, such as proteins, can be applied, e.g., spread,at the air-water interface from a detergent solution onto a lipid film.Other methods of applying the protein include applying a nativepreparation of lipid membrane or proteoliposomes preferably includingover-expressed amounts of the desired protein. Alternatively, theprotein can also be applied using reconstituted protein-lipid liposomepreparations. Preparation of the proteoliposomes is done by thedetergent dialysis technique of Mimms et al., using an appropriateprotein to lipid ratio (Biochem. 20, 833-840 (1981)).

This invention is further illustrated by the following examples whichshould not be construed as limiting. The contents of all references andpublished patents and patent applications cited throughout theapplication are hereby incorporated by reference.

EXEMPLIFICATION OF THE INVENTION Example 1 Direct Visual Evidence forthe Formation of Ordered Structures, e.g., Large Ordered Domains, of aMembrane Proteins at an Air-Aqueous Interface

In this example, a unique ability to grow ordered structures of amembrane protein on a liquid in a fast and controlled fashion isdemonstrated. The membrane protein cytochrome c oxidase (COX) from beefheart was chosen as a model membrane protein to elucidate thefeasibility of the technique. The structure of COX has been extensivelystudied in different laboratories. The structure of the metal sites ofCOX was determined to 2.8 Å resolution by x-ray analysis (Tsukihara, T.,et al. Science 269, 1069-74 (1995)). Crystal structure information atintermediate resolutions is available of tetragonal or hexagonalbipyramidal crystals that diffract x-rays to 5 Å (Shinzawa-Itoh, K., etal. J. Mol. Biol. 246, 572-575 (1995)) and 8 Å (Yoshikawa, S. et al.PNAS, 85, 1354-1358 (1988); Yoshikawa, S., et al. J. Crystal Growth,122, 298-302 (1992)) respectively. The structure of COX is also known,at low to intermediate resolution, from image processing of electronmicrographs of two-dimensional crystals of the protein (Frey, T. G.Microscopy Research and Technique 27, 319-332 (1994)). Two such crystalforms have been reported, one consists of dimers (Henderson, R. et al.J. Mol. Biol. 112, 631-648 (1977)) and a second consists of monomers ofCOX (Fuller, S. D. et al. J. Mol. Biol. 134, 305-327 (1979)). In bothcases, these in-situ crystals of the protein are so small that theycannot be resolved with high resolution electron microscopy. Instead,researches have used elaborate image processing techniques to indirectlyprovide insight into the structure of the protein. The dimer crystalform of

COX has been most extensively studied. Cryoelectron microscopy analysisof Valpuesta et. al. extended the earlier structure information ofHenderson and coworkers to 8-10 Å resolution in the plane of themembrane and to 15 Å perpendicular to it (Valpuesta, J. M. et al. J.Mol. Biol. 214, 237-251 (1990); Henderson, R. et al. J. Mol. Biol. 112,631-648 (1977)). These results revealed that the two-dimensional spacegroup for the dimer is pgg, the two-sided plane group p22 ₁ 2 ₁, withcell dimensions a=95 Å, b=125 Å, γ=90°. The crystals of COX monomerswere characterized by Fuller et al. (Fuller, S. D. et al. J. Mol. Biol.134, 305-327 (1979)). They concluded that the crystals are packed in asingle layer. The two-dimensional plane group is pg with unit cellconstants of a=68 Å and b=174 Å, and corresponding to the two-sidedspace group p12₁.

In the following example, the process for lining up COX molecules at anair-aqueous interface, is described. Formation of ordered structures ofthe protein is demonstrated by digital laser fluorescence videomicroscopy. It is also shown the shape of these domains often appears tobe directly related to the known configuration of the individual proteinmolecules. Unexpectedly, three-dimensional ordered structures of theprotein at the air-aqueous interface were also formed. The degree oforientational order of these microstructures by parallel x-ray as wellas electron crystallography is currently being investigated. Thefollowing example is a preliminary characterization of the factors thatgovern formation of ordered domains of the protein at the air-aqueousinterface.

Techniques Chemicals and Biochemicals

Biotinilated cytochrome c (B-CC), and fluorescein isothiocynateconjugated avidin (FITC-A) were from Sigma. Fluorescein isothiocynateconjugated streptavidin (FITC-SA) was purchased from Biomeda Corp.(Foster City, Calif.). Fluorescently labeled lipidsL-α-Phosphatidylethanolamine-N-(lissamine rhodamine B sulfonyl) (Egg)(R-PE), and1-Acyl-2-{12-{(7-nitro-2-1,3-benzoxadiazol-4-yl)amino}dodecanoyl}-sn-glycero-3-Phosphatidylethanolamine(NBD-PE) were from Avanti Polar Lipids (Alabaster, Ala.).

Membranous COX was a generous gift of Professor T. G. Frey, San DiegoState University. The membranes were prepared using the method developedby Frey et al. (J. Biol. Chem. 253, 4389-4395 (1978)). The material wasin the form of proteoliposomes, with a high concentration of protein,10-15 mg protein/ml, and approximately 3-5 mg phospholipid/ml (T. G.Frey personal communication). They were suspended in 10 mM potassiumphosphate buffer, pH 7.2, including 0.25 M sucrose. The material wasreceived on dry ice and transferred to −80° C. upon arrival. Samples forcrystallization experiments were prepared by rapidly thawing the stockunder flowing water at room temperature. Aliquots were made in 1.5-mlmicrofuge tubes after diluting the stock ten times. The tubes were oftenrapidly frozen under liquid nitrogen, prior to their transfer to −80° C.for storage. An aliquot of the proteoliposome suspension was thawed,under running water at room temperature, immediately before thecrystallization experiment, and used within the same day.

Preparation of Protein Microdomains at an Air-Aqueous Interface

A suspension of the proteoliposomes was spread at the air-aqueousinterface of the Micro-Trough MT-100 equipped for digital laserfluorescence video microscopy. The proteoliposomes were spread againstan increasing surface pressure by using a modified form of the proceduredescribed earlier by Verger and Pattus (Chemistry and Physics of Lipids16, (1976)). Prior to each experiment, the trough was assembled by usingclean components, including the Kalrez barriers, the quartz platecomprising the bottom of the trough, the Teflon rings comprising theside walls and the O-ring seals that prevent subphase leakage. Surfacepressure was measured by using the Wilhelmy method. The Wilhelmy platewas cut from Whatman No. 2 paper. A new plate was used for eachexperiment. The trough was filled with a hypotonic buffer including 10mM phosphate, pH 7.2. The buffer was prepared fresh daily by using acontinuos flow ultra pure water system and stored in a glass container.A clean sintered glass slide was inserted into the subphase and made wetwith the buffer to about 1 cm above the water line. The proteoliposomes,with their internal as well as external volumes composed of a hypertonicbuffer including 10 mM phosphate and 0.25 M sucrose pH 7.2, weredeposited onto the pre-wetted areas of the glass slide via a glassmicropipette.

The working area of the trough was kept constant, around 40-44 cm²during the spread of the proteoliposomes. Upon encountering thehypotonic subphase buffer, the proteoliposomes lysed and spread as aplanar membrane at the air-aqueous interface. Formation of the planarlipid-protein film was evidenced by an abrupt rise in surface pressure.Excess amounts of the proteolipo some suspension were deliveredsequentially, to a final bulk concentration of 50-150 μg/ml in proteinand 15-50 μg/ml in lipid in a total volume ranging between 6-12 ml. Anequilibrium pressure was achieved between the spread film and theunlysed proteoliposomes where further additions of proteoliposomes didnot cause a substantial increase in surface pressure. The range of theequilibrium pressure varied between 20 to 38 mN/m. Subsequent toestablishing the equilibrium, excess unlysed proteoliposomes were washedaway from the lipid-protein film, by several vigorous exchanges of thesubphase with fresh hypotonic buffer. A 5-10 mN/m drop in surfacepressure was observed, during the removal of the proteoliposomes. Thelipid-protein film was compressed at a rate of 500 mm²/min, fromapproximately 40 to 11 cm², to a maximum density corresponding topressures between 35-45 mN/m.

Preparation of Ordered Protein Microdomains for Fluorescence Imaging:Double Labeling of the Lipids and Protein.

The lipid molecules in the lipid-protein film were probed with thefluorescent lipid probe R-PE. A dilute film of about 1 μg of R-PE wasspread from a dichloromethane solution on a clean subphase including 10mM phosphate, pH 7.2. Subsequent to the evaporation of the solvent theproteoliposomes were spread and the excess unlysed material was removedas described above. COX was fluorescently probed, at the air-aqueousinterface, with FITC by producing a ternary complex, between COX, B-CCand FITC-SA (FITC-A). The complex was formed in two steps. Initially, abinary complex was formed between COX and B-CC, by injecting a solutionof B-CC in buffer, through the lipid-protein film into the subphase to afinal concentration of 50-100 μg/ml. After an incubation period of 5-20minutes, excess B-CC was washed away from the film by several exchangesof the subphase with fresh buffer. In the next step, a ternary complexwas formed between COX-B-CC and FITC-SA (FITC-A), by injecting asolution of the FITC-SA (FITC-A), through the lipid-protein film to afinal concentration of 10-20 μg/ml. After an incubation period of 5-20minute, unbound FITC-SA (FITC-A) was removed in the same manner asdescribed for the removal of unbound B-CC.

Digital Fluorescence Video Imaging and Image Processing System

The Micro-Trough MT-100 was mounted on the stage of an Olympus IMT-2,equipped with epi-illumination optics. Fluorescence emission from boththe rhodamine as well as the FITC probes was excited with the 488 nmline of an air-cooled argon laser (Ion Laser Technology Systems, SaltLake City, Utah). Using an Olympus DPlan x10 (N.A. 0.25) or CDPlan x40(N.A. 0.50) ultralong working distance objectives the fluorescentdomains were imaged at the air-aqueous interface, as well as throughouttheir transfer to solid supports. The x40 objective was equipped with a0.0-2.0 mm correction collar that facilitated high resolution imagingthroughout the height of the subphase in the trough. By adjusting theobjective collar to an appropriate height, the film was visualized atthe air-aqueous interface, through a 1-mm quartz plate located at thebottom of the MT-100, and a 0.5-0.7 mm depth of subphase. Films weretransferred to a solid support at the air-aqueous interface oralternatively were deposited onto the quartz plate at the bottom of thetrough. Deposition of the film onto the solid substrate could bevisually monitored throughout the transfer process by using the sameoptics. Fluorescence emission from both the FITC and rhodamine probespassed through a 505-nm dichroic long pass filter (505DCLP) (ChromaTechnology Corp., Brattleboro, Vt.), and subsequently through a 515-nmlong pass emitter (OG515) (ibid.). Digital laser fluorescence videoimage acquisition and processing was done by using the system describedabove.

Preparation of Specimens for Electron Crystallography

Specimens for electron crystallography analysis were prepared fromplanar membranes of COX both in the presence of the ternaryprotein-ligand complex as well as in its absence. This strategy allowedfor the effect of the interaction of the ligand (B-CC) and thefluorescent protein probe (FITC-SA) on the crystal structure of COX tobe determined. The lipids in the lipid-protein film were labeled witheither the lipid probe NBD-PE or R-PE as described before. The orderedstructures were transferred from the air-aqueous interface to 200 meshcopper electron microscope grids by horizontal deposition. The gridswere pre-coated with either a hydrophilic (silicon oxide) or hydrophobic(carbon) film. They were placed horizontally on top of the orderedstructure for 5-10 minutes, and removed from the interface with a pairof tweezers. The grids were air-dried prior to their transfer to a gridbox for storage. The stored ordered structures were analyzed within 30days from their preparation.

Electron Microscopy and Diffraction Analysis

Preliminary electron microscopy and diffraction analysis experimentsmade use of the MRSEC Shared Experimental Facilities supported by theNational Science Foundation under award number DMR94-00334. Electronmicrographs from unstained ordered structure were recorded at roomtemperature at 200 kV in a Joel 200CX microscope. Significant beamdamage to the ordered structure was observed under these experimentalconditions. In order to avoid prolonged ordered structure irradiationduring the recording of an image on film, images were recorded at videorate on a videocassette. Diffraction patterns as well as bright and darkfield images were later captured from the videotape by using the digitalimage processing system described in subsequent sections. However, sincethe images still exhibited considerable beam damage, follow upexperiments are postponed to the use of a high voltage, low-temperatureelectron microscope facility.

Subsequent electron micrographs and diffraction patterns were recordedfrom unstained ordered structures, in an AEI-EM7 high-voltage electronmicroscope, equipped with a Gatan 626-cryotransfer stage. The imageswere recorded at room temperature, on MRF32 film at 1200 kV. Themicroscope was equipped with a Pulnix intensified CCD camera, whichproduces images at video rate from low beam dose rates at about 2×10⁻¹¹amp. This allows scanning the specimen and focusing using minimalirradiation. The selected area was located by scanning in diffractionmode with negligible electron exposure at approximately 2×10⁻¹² amp. Thelow dose exposure is estimated to be approximately 10 electrons/Å². Whenan area was found that produced a high-resolution zone-axis pattern, thebeam was turned off, film was transported into the camera, and the beamwas turned on only when the camera shutter had opened. Electronmicrographs were obtained subsequently from the selected area. Thisprocedure minimized electron damage to the crystals prior to therecording of the diffraction pattern. The film was developed for fourminutes in XRD developer at 20° C., which gave an acceptable density atthe low exposure. Subsequent to the recording of an electron diffractionpattern, a bright field image of the same selected area was recorded onfilm.

Results and Discussion

The structure of COX was analyzed qualitatively by fluorescence imagingas well as electron crystallography. Digital laser fluorescence videoimaging revealed formation of ordered structures of COX in planarmembranes spread at an air-aqueous interface.

Ordered structures were observed by fluorescence, in planar membranesspread from proteoliposome preparations of COX at the air-aqueousinterface. The proteoliposomes were spread against an increasing surfacepressure in order to minimize surface denaturation of the protein. Theplanar protein-lipid membrane (which contained the ordered structures)was stained with two different labels to bring out the contrast betweenthe lipid and protein species. The protein was stained with FITC-SA(FITC-A) bound to a B-CC-COX complex. The lipids were stained with R-PE.All films reported in these studies were formed at ambient temperature(22±2° C.), over a buffer subphase including 10 mM phosphate, pH 7.2.The protein ordered structures were observed using an x10 or x40objective. They appear green in an orange background made by thefluorescent lipid probes partitioning the lipid domains of the film. A0.2 second on chip integration time was used on the camera to producethese images. The ordered structures reported here were observed at asurface pressure corresponding to 16 mN/m. On the left in FIGS. 7A, 7C,and 7E, it was demonstrated by fluorescence some of the many orderedstructures that were generated. These ordered structures exhibit severaldistinct features. Most notable is the remarkable similarity between theshape of these ordered structures and the images of the crystals of COXcalculated from electron microscopy analysis as shown on the right inFIGS. 7B. 7D, and 7F.

The fluorescence micrograph in FIG. 7A provides direct visual evidenceof the morphology of a rectangular ordered structure consistent with theknown shape of a dimer molecule. In comparison, FIG. 7B shows an imageof a single COX dimer calculated by Frey and coworkers, from electronmicrographs of frozen hydrated crystals (Frey, T. G. & Murray, J. M. J.Mol. Biol. 237, 275-297 (1994)).

The monomer crystals of the protein have a different appearance than thedimers. Fuller et al. characterized this crystal form. The shape of themolecule is represented by a lower case letter y from their balsa woodmodel. FIG. 7C is a fluorescence micrograph of a COX domain resemblingthe shape of the protein in its monomeric form, calculated by Frey andMurray (FIG. 7D). FIG. 7E is a protein domain observed by fluorescencethat is remarkably similar to the y shape crystal form of the protein(FIG. 7F), taken from the three-dimensional reconstruction of Fuller etal.

The orientation of proteins at the air-aqueous interface sometimesappears to be perpendicular to the expected orientation of the proteinmolecules in the cell membrane (see FIGS. 7A-F). It is not clear whatfactors govern the orientation of the protein at the air-aqueousinterface. The protein molecules may re-orient at the air-aqueousinterface during their spread at low packing densities. Alternatively,the orientation of the domains may be indicative of the formation ofmultilamellar structures at the air-aqueous interface. This effect canbe studied by measuring the thickness of the film at different packingdensities, may be better understood.

Other forms of COX domains were also observed at the air-aqueousinterface. The detailed shape of these domains provides further insightinto several other distinct features of the structure of the COXmolecule. Of particular interest in some fluorescence micrographs, was ahole or slit that appeared as an isolated lipidic phase (orange) withinthe protein domain. The hole or slit may be attributed to the presenceof a cleft in the dimer that separates its two monomer halves. The cleftin the dimer was previously suggested by Costello and Frey (J. Mol.Biol. 162, 131-156 (1982)). The trigonal symmetry of the hole as shownin certain contours of the domains was also shown. Sometimes, themicrographs show COX structures which show the domains split apart,consistent with earlier electron microscopy results of Frey andcoworkers.

In producing the micrographs, image enhancement was used to help the eyedifferentiate between the fluorescent molecules. It is believed thatimportant information may be inferred from these colors. For example, inimage enhanced micrographs, areas around the periphery of the proteindomains sometimes appear to have a darker green contrast than in themiddle. The darker contrast is attributed to self-quenching offluorescein molecules in a densely packed protein array. Also, ofinterest in some of these micrographs is the presence of a brightorange-red halo around the protein ordered structures (FIGS. 7A-7F). Thehalo may be indicative of the existence of lipid-embedded domains in theindividual COX molecule. Thus, the enhancement of contrast in the halois probably due to energy transfer from bound FITC protein complex torhodamine tagged lipid probes residing within a close proximity of theprotein in the lipid-embedded domains. The existence of thelipid-embedded domains was suggested by Frey from observation ofice-embedded specimen of COX crystals. Similar observations were made byBrisson and Unwin in electron micrographs of specimen of acetyl cholinereceptor frozen in vitreous ice, showing denser protein domainscontrasted by less dense ice or lipid domains (Brisson, A. & Unwin, P.N. T. Nature, 315, 474-477, (1985)).

The excellent contrast between the protein ordered structures and lipiddomains, in the fluorescence micrographs in FIGS. 7A-7F, is a result ofquenching of background fluorescence due to energy transfer from FITC tothe rhodamine probes. Specifically, enhancement of contrast was due toquenching of fluorescence that was originated from those FITC moleculesthat were either nonspecifically bound to the lipids or lowconcentrations of unbound molecules floating in the subphase, below thelipid film. Confirming this hypothesis, in control experiments, muchlower contrast was observed, when the film was probed with FITC-SA inthe absence of the rhodamine labeled lipid. The protein orderedstructures were hardly visible in the somewhat homogeneous green planarmembrane, due to substantial background fluorescence. Low contrast wasalso observed when the planar membrane was probed with a lipid probeonly. The somewhat homogeneously orange appearance of these films wasprobably due to the rhodamine lipid probes that partitioned the lipiddomains as well as those lipid probes that stained the proteinmolecules. Under certain conditions, in these single probe studies, darkpatches of loosely packed protein domains, with no specific symmetrywere also observed.

The ordered structures, e.g., solid phase domains are formed at theair-aqueous interface probably due to a long-range orientational order.Weis and McConnell showed that such an order is essential for formationof chiral crystals on compression of lipid monolayers ofdipalmitoylphosphatidylcholine at an air-water interface (Weis, R. M. &McConnell, H. M. Nature, 310, 47-49 (1984)). It is speculated that ahigh protein/lipid ratio in the proteoliposome may facilitate theformation of the ordered structures. Pattus and co-workers in spreadingof biomembranes at an air-water interface report that the surfacedensity of the protein increases, when membranes are spread at highersurface pressures (Pattus, F. et al. Biochim. Biophys. Acta 507, 71-82(1978)).

Digital laser fluorescence imaging reveals formation ofthree-dimensional ordered structures on compression of a lipid-proteinfilm of COX at an air-aqueous interface. The detailed shape of theprotein ordered structures is a sensitive function of the packingdensity within the lipid-protein film. At higher pressures (e.g., about40 mN/m), a slight drop in pressure during the pause was observed. Thiscan be seen as a point of discontinuity in the pressure-area isotherm. Areduction in size of an ordered structure, due to a compression inducedincrease in the packing density of the molecules was observed. Aremarkable feature of the compression of the lipid-protein film is acritical density point around 34 mN/m. At this point one observes byfluorescence a drastic rearrangement of the molecules in the film.Further compression of the film beyond the critical density pointresults in formation of small (20-50 μm diameter) ordered structureswith a three-dimensional (3-D) appearance. The three-dimensional shapefor these ordered structures, was particularly noticeable after theordered structures were transferred to a solid substrate. Thethree-dimensional shape of the domains was noted with the out of focusdepth in these micrographs. New x-ray microdiffraction technologies thatincorporates an intense microbeam source of radiation is being used todetermine the degree of structural order in these three-dimensionalordered structures.

It is interesting to note that, in their earlier studies on the brushborder membrane, Demel et al. attribute a surface pressure of 35 mN/m tothe lateral pressure in the native membrane (Demel, R. A. et al.Biochim. Biophy. Acta 406, 97-107 (1975)). By analogy, a correlationbetween the critical density observed around 34 mN/m in the planarmembrane was drawn to the to the lateral pressure of the nativemembranes of COX.

Recently, Rein ten Wolde and Frenkel suggested an enhancement of proteincrystal nucleation by critical density fluctuations (Science 277,1975-1978 (1997)). Their numerical simulation for certain globularproteins suggests that close to a critical point, the free-energybarrier for crystal nucleation is strongly reduced and hence, thecrystal nucleation rate is increased by many orders of magnitude. Animplication of their findings is that one can selectively speed up therate of nucleation, without increasing the rate of crystal growth, orthe rate at which amorphous aggregates form. This can be achieved insolution by changing for example the composition of the solvent. Theformation of cholesterol crystals at an air-aqueous interface providedirect evidence on the extension of this rule to a system intwo-dimensions. In that example, a direct correlation betweensupersaturation beyond a metastable critical density point and thecrystal nucleation process was noted. Specifically, no crystals wereformed by rapidly compressing the monolayer way beyond the metastablecritical density point. In this example, the formation of a certainpopulation of domains immediately above a critical density point wasobserved. It is therefore, reasonable to expect that the methods of theinvention provide an ideal framework to extend the general theoreticalderivations of Rein ten Wolde and Frenkel to protein systems intwo-dimensions.

Example 2 Electron Microscopy and Electron Diffraction of OrderedDomains Prepared at an Air-Aqueous Interface

Ordered structures of the protein COX were formed at an air-aqueousinterface for structure analysis by electron crystallography. Theordered structures were transferred to hydrophobic (carbon-coated) orhydrophilic (silicon oxide coated) grids. Two different types ofspecimen preparations were used for comparative analysis. In certainspecimens, a complex was made between the protein, B-CC and FITC-SA.However, these probes were excluded in a majority of specimenpreparations in order to eliminate the effect of bound ligands on thestructure of the protein. In all specimen ordered structures, the lipidswere probed with the fluorescently tagged lipid R-PE. Inclusion of thelipid probe facilitated visual monitoring of the ordered structureduring its transfer to the grids. The electron microscope studiesreported here were done on unstained specimen, at room temperature(22±2° C.), by using either 200 or 1200 kV electron beams.

Consistent with the fluorescence studies, direct visual evidence on thepresence of ordered structures was obtained by electron microscopy. Theprotein ordered structures that were deposited on the grids were up to110 μm² in area. Although these domains were significantly smaller thanthose observed at the air-aqueous interface, they appeared to presentthe same overall morphology as their larger counterparts. It is notuncommon to obtain a smaller domain size on films transferred to a gridin comparison to that at an air-aqueous interface. In preparation ofelectron microscope grids from crystals of a soluble protein on a lipidmonolayer, Darst et al. report a similar behavior (Biophys. J. 59,387-396 (1991)). They speculate that the smaller crystals are derivedfrom the larger domains at the air-aqueous interface, but are brokenapart during the transfer process due to the stresses involved therein.

The morphology of these domains that were transferred to the grid isreminiscent of the three-dimensional representation of a single monomeror dimer molecule as explained above. In some cases, typical rectangularor y-shaped domains were observed. Another remarkable feature of theelectron micrographs is the appearance of two different regions withinthe protein ordered structure. This is consistent with the observationof a bright halo around the protein in some fluorescence micrographsshown in FIGS. 7A-7F. The brighter contrast observed around the proteinordered structure was attributed to the presence of less denselipid-embedded domains around single protein molecule. The darkercontrast observed in the central regions is probably due to the presenceof densely packed protein molecules. In this example, it was observedthat the densely packed regions were more prone to electron beam damage,than the less dense lipid-embedded areas surrounding the protein.

Electron diffraction analyses of the ordered structures of COX provideevidence on different features of the specimen preparation technique. Incertain areas of the grids, distinct diffraction spots were observed,that were extremely resistant to beam damage. The lattice spacingcalculated from such diffraction patterns was on the order of 5-10 Åwhich is smaller than the larger distances expected from a proteinmolecule (typically 100 Å). These results indicate the presence of smallorganic or inorganic crystals such as salt or silicates in the specimen.At the bottom are bright field electron micrographs of the selectedarea, showing an epitaxial growth of the crystalline material. Thesemicrographs were taken from films transferred to a silicon oxide gridaround 18 mN/m. Occasionally, during the scan of the specimen, sharpdiffraction spots were encountered which rapidly faded away before beingrecorded on film. In view of their sensitivity to beam damage, thesespots are attributed to the presence of crystalline protein domains thatdeform or dehydrate under the electron beam. This example may berepeated by preparing frozen-hydrated specimens for cryoelectrondiffraction analysis of the protein. However, if the protein forms havea three-dimensional morphology, they will not diffract electrons. Thus,x-ray diffraction analysis by using an intense microbeam source ofradiation may also be used. The remarkable long-range orientationalorder observed in these ordered structures, suggests that thesestrategies may provide a means to determine, for the first time, thethree-dimensional structure of the COX in ordered domains made in anatural membrane at an air-aqueous interface.

Conclusions

Formation of ordered two-dimensional or three-dimensional structures atan air-aqueous interface has not been previously reported for anymembrane protein. The experiments discussed here demonstrate thefeasibility of a novel approach for fabrication of ordered orderedstructures of the membrane protein COX at an air-aqueous interface.These studies lead to the following conclusions. (i) At intermediatepressures, corresponding to 10-30 mN/m, and below a critical densitypoint, the membrane protein COX arranges at the air-aqueous interface inlarge, ordered forms. The detailed shape of the protein orderedstructures often appears to be directly related to the knownconfiguration of individual protein molecules both in their monomer anddimer forms. (ii) At high pressures beyond a critical density point, theformation of a different population of domains consisting of smallerthree-dimensional ordered structures were observed.

This example provides evidence of the presence of ordered structures.This was shown by the fast fading spots that were observed in electrondiffraction analysis of unstained specimen taken at room temperature. Intwo different lipid systems, ordered structures were shown to grow atthe air-water surface.

Electron diffraction analysis of the protein ordered structures willcontinue in order to determine the degree of orientational order in theprotein domains. These studies are conducted at cryogenic temperatures,to reduce radiation damage to the protein. The results do not rule outthe possibility that the large domains, formed below the criticaldensity point, may also be three-dimensional ordered structures.Parallel x-ray diffraction studies, by using an intense microbeamsource, will allow the probing of the structure of this population ofordered structures.

Fabrication of ordered two-dimensional and three-dimensional domainsfrom membranes is not only relevant to the rational design of drugs withmolecular modeling based on high-resolution three-dimensional structureof the target protein, but it may also play a key role in proteomics toaccelerate drug discovery via structure activity relationships (SAR).The fluorescence imaging studies, provide direct visual evidence onbinding of a high affinity ligand, such as the cytochrome c to COX. Thiswas evidenced by a qualitative fluorescence assay based on fluorescencevisualization of formation of a ternary complex between COX, B-CC andFITC-SA. This example showed that ordered protein ordered structures canbe formed both in the absence of the ligand as well as in the presenceof a ligand bound protein complex.

Example 3 Direct Visual Evidence for Formation of OrderedTwo-Dimensional Ordered Structures of the Multidrug ResistanceP-Glycoprotein

In another system, comprised of the multidrug resistance P-glycoprotein(P-gp), the formation of large ordered domains of the protein in itsnatural membrane was demonstrated. Non-random distribution of cellsurface P-glycoprotein (P-gp) in monolayers spread from multidrugresistant MCF-7 Adr^(R) and MCF-7 sensitive cell lines was shown. Cellmembrane vesicles were prepared according to the method of Cornwell etal. (J. Biol. Chem. 261, 7921-28 (1986)). Monolayers were spread fromvesicles in a hypertonic buffer including a high concentration ofsucrose. The vesicles were spread at the air-aqueous buffer interface ofthe Micro-Trough MT-100, on a hypotonic buffer in the same manner as itwas discussed earlier for COX. Spreading of the monolayer was monitoredby observing an increase in the surface pressure of the spread film at aconstant area. P-gp was probed with a fluorescent derivative ofverapamil, a calcium channel blocker that binds to P-gp. Fluorescencemicroscopic observation of P-gp in monolayers spread from drug resistantcell membranes suggests strong long-range orientational order of theprotein in monolayer, induced by compression. This led to formation ofdensely packed domains of the protein, which may eventually lead to itscrystallization. No such domains were observed in control experiments inmonolayers spread from drug-sensitive cell membranes. This may be due topresence of negligible amounts of protein in drug-sensitive MCF-7preparations in contrast to drug-resistant membranes.

The total amount of P-gp in the drug resistant MCF-7 Adr^(R) plasmamembrane preparations is estimated to be as little as 2%. These resultstherefore suggest that extremely high concentrations of the protein maynot be essential for fabrication of crystals by monolayer compression.

The structure of P-gp was recently solved to 25 Å resolution (Rosenberg,M. F. et al. J. Biol. Chem. 272, 10685-94 (1997)). The shape of thelarge domains we produce was remarkably reminiscent of the molecularoutline of P-gp proposed by Rosenberg et al. The aqueous pore, open atthe extracellular face of the membrane, was clearly evident in bothimages. The fluorescence micrograph also provides evidence on the shapeof the thumb-shaped domains (TMD) as well as the nucleotide bindingdomains (NBD).

Two-dimensional crystallization within the membrane, in comparison withtwo-dimensional and three-dimensional crystallization from solution hassome advantages. Since the protein does not dissociate from the lipidbilayer, the native asymmetry of the membrane is maintained. Therestricted freedom of movement in the planar membrane means that thechances of lattice formation are higher than for crystallization from anisotropic solution. Usually, the protein is not exposed to high levelsof detergent and is therefore more stable. In bilayers, possibilitiesfor improving the crystallization conditions by varying experimentalparameters are limited. However, monolayer compression provides thenecessary tool for rearranging the molecules in both natural as well asreconstituted membranes.

Example 4 Direct Visual Evidence for the Nucleation of CholesterolCrystals at an Air-Water Interface near a Metastable Critical DensityPoint

Cholesterol appears in animals in certain cell membranes, bound tolipoprotein or incorporated in the bile micelles. Crystals ofcholesterol monohydrate deposit when cholesterol levels are unusuallyhigh. In bile, these crystals stack up to form gallstones. Cholesterolmonohydrate crystals also occur in arherosclerotic lesions. Thecholesterol molecule is an ampiphile. It is almost hydrophobic exceptfor the presence of a hydrophilic C(3) hydroxyl group. This amphiphiliccharacter of the molecule allows it to position itself at polar-nonpolarinterfaces.

The structure of cholesterol has been extensively studied, both in ananhydrous as well as a monohydrate form. Craven reported the crystalstructure of cholesterol monohydrate, in crystals grown fromacetone-water solution (Craven, B. M. Nature 260, 727-729 (1976)). Theoverall structure is a stacking of bilayers of thickness d₀₀₁=33.9 Å°.The crystals are triclinic. The space group is P1, with reduced cellparameters a=12.39, b=12.41, c=34.36 Å°, α=91.9, ↑=98.1, γ=100.8°. Shiehet al. solved the structure of anhydrous cholesterol (Shieh, H. S. etal. Nature 267, 287-289 (1977)). They reported formation of lath-shapedcrystals obtained by cooling a saturated acetone solution ofcholesterol. The anhydrous crystal is also triclinic. The space group isP1, with reduced cell parameters a=14.00, b=33.71, c=10.46 Å°, α=94.5,β=90.0, γ=95.9°.

This example demonstrates a unique approach to growing crystals ofcholesterol by compression of a monolayer at an air-water interface,near a metastable critical density point. The ordered structuresproduced by this technique were large (25-50 μM in diameter), flat,highly ordered and diffracted electrons to atomic scale resolution. Theresults of this example, reveal a direct correlation between the degreeof supersaturation in two-dimensions, beyond a metastable criticaldensity point, and the cholesterol crystal nucleation process. TheLangmuir technique was used as a tool to organize the amphiphiliccholesterol molecules at an air-water interface and subsequentlycompress them in two-dimensions to and beyond a critical density point.

Monolayers composed of a binary mixture containing cholesterol (>99%;Nu-Check-Prep, Inc., Elysian, Minn.), and 0.9 mole % of the fluorescentlipid probe L-α-Phosphatidylethanolamine-N-(lissamine rhodamine Bsulfonyl) (Egg) (R-PE), or 1.6 mole % of the fluorescent lipid probe1-Acyl-2-{12-{(7-nitro-2-1,3-benzoxadiazol-4-yl)amino}dodecanoyl}-sn-glycero-3-Phosphatidylethanolamine(NBD-PE) (both probes from Avanti Polar Lipids, Alabaster, Ala.), wereformed at the air-water interface of the microscope mountable monolayertrough the Micro-Trough MT-100 (Ultrathin Film Technology, Ltd.,Cambridge, Mass.). The trough was mounted on the stage of an OlympusIMT-2 microscope, equipped with the digital laser fluorescence videomicroscopy system described above. Fluorescence emission was excitedwith the 488 nm line of an air-cooled argon laser (Ion Laser TechnologySystems, Salt Lake City, Utah). The fluorescent domains were imaged atthe air-water interface, by using an Olympus DPlan x10 (N.A. 0.25) orCDPlan x40 (N.A. 0.50) ultralong working distance objectives. Allmonolayers were formed at ambient temperature (20±2° C.), over anultra-pure water subphase. Ordered structures were transferred, from theair-water interface, to 200 mesh copper electron microscope grids coatedwith silicone oxide. Deposition of the ordered structures onto thesubstrates was monitored by fluorescence, throughout the transferprocess. The degree of ordering in the ordered structures was analyzedby selected area electron diffraction of the deposited orderedstructures. The electron diffraction studies were done on unstainedspecimen, at room temperature, by using the 1200 kV electron microscopefacility at the Wadsworth Center, Albany, N.Y.

The cholesterol monolayer was compressed at a rate of 200 mm² per minuteat the air-water interface. At low packing densities, and up to acharacteristic limiting area around 36 Å² per molecule, the isothermexhibits the characteristics of a highly compressible monolayer. Thelimiting area is to some extent affected by temperature fluctuations,the amount and composition of the fluorescent lipid probes in the binarymixture, as well as the errors involved in weighing and handling smallquantities of material. The average limiting area reported in this studyis consistent with a cross sectional area of 36.2 Å² per molecule ofcholesterol, calculated by Craven from x-ray crystallographic analysis(Craven, B. M. Nature 260, 727-729 (1976)).

Further compression of the film, beyond the limiting area results nosignificant change in the film pressure. However, by fluorescence,formation of two different domain shapes was observed as a result ofcompression beyond the limiting area. At a critical density point anintermediary metastable phase was observed. This phase often appeared atan apparent area per molecule around 27 Å², half way between thelimiting area (around 36 Å² per molecule) and a characteristic area(around an apparent area at 18 Å² per molecule) where the molecules areexpected to be stacked in a bilayer. The term “apparent area permolecule” is used here instead of “area per molecule” since at highpacking densities, beyond the limiting area, the film is no longermonomolecular. Complex metastable patterns were produced around thecritical density point. Further compression of the film, at a slow ratetoward the characteristic bilayer area, produced a transformation in theshape of the patterns into plate-like parallelograms usually including anotch at some corners. The shape of the plate-like ordered structures isremarkably reminiscent of the shape of the crystals of cholesterolmonohydrate. Under certain conditions, near the critical density point,a time-driven transformation of the metastable domains into theplate-like ordered structures was observed. These results indicate adirect correlation between the crystal nucleation process and the degreeof super-saturation near the metastable critical density point. Thisrelationship was further supported in control experiments where nocrystals were formed if the film was compressed rapidly far beyond themetastable critical density point.

Electron diffraction analysis of the ordered structures transferred to amicroscope grid, near the critical density point, provides evidence forthe presence of highly ordered crystal domains of cholesterol, byexhibiting distinct diffraction spots. The diffraction pattern was takenfrom a ordered structure transferred to a silicon oxide grid near thecritical density point around 27 Å² per molecule. The diffraction spotsin the film were extremely resistant to beam damage. The calculatedspacing from the diffraction spots in this pattern, was approximatelya=13, b=17 Å. It is possible that the spots along the b axis originatefrom every other reciprocal lattice element in the repeat. If so, thiswould correspond to a doubling of the distance in the direct latticeparameters along the b axis; i.e. b=34 Å. In that case, the result willbe remarkably consistent with the lattice parameters, reported by Shiehet al., for anhydrous cholesterol crystals; i.e. a=14.00, b=33.71 Å(Shieh, H. S. et al. Nature 267, 287-289 (1977)). FIGS. 4-3A,B showsbright field electron micrographs of the selected area.

It is quite unexpected that two-dimensional crystals of cholesterol tobe formed by compressing a monolayer beyond a metastable criticaldensity point. This method provides an ideal framework to extend thegeneral theoretical derivations of Rein ten Wolde and Frenkel onenhancement of crystal nucleation by critical density fluctuations, tosystems in two-dimensions (Rein ten Wolde, P. & Frenek, D. Science 277,1975-1978 (1997)). A better theoretical understanding of the effectsthat underlie these empirical results may lead to a general rule forimplying this powerful approach towards producing large and orderedcrystals for other constituents of biological membranes, such asmembrane proteins. Controlled fabrication of two-dimensional crystals ofcholesterol, at an air-water interface, may provide further insight intothe mechanism of cholesterol crystallization in vivo. This method isalso expected to prove useful for screening drugs that promote orinhibit the cholesterol nucleation process

Equivalents

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments and methods described herein. Such equivalents are intendedto be encompassed by the scope of the following claims.

All patents, patent applications, and literature references cited hereinare hereby expressly incorporated by reference.

1.-28. (canceled)
 29. A method for determining the shape of anamphiphilic molecule, comprising contacting a population of saidmolecule with a interface; compressing said population to an appropriatepressure, such that an ordered structure is formed at said interface,and analyzing said ordered structure such that the shape of saidamphiphilic molecule is determined.
 30. The method of claim 29, whereinsaid population of amphiphilic molecules comprises proteins,glycoproteins, glycolipids, or steroids.
 31. (canceled)
 32. The methodof claim 30, wherein each of said proteins is a membrane protein, acellular receptor, an orphan receptor, receptor tyrosine kinase, an EPHreceptor, an ion channel, a cytokine receptor, an multisubunit immunerecognition receptor, a chemokine receptor, a growth factor receptor, ora G-protein coupled receptor.
 33. The method of claim 29, wherein saidordered structure is two-dimensional.
 34. The method of claim 29,wherein said shape is determined by electromagnetic radiation.
 35. Themethod of claim 34, wherein said electromagnetic radiation is selectedfrom the group consisting of light, electrons, x-rays, neutrons, orgamma rays.
 36. The method of claim 34, wherein said shape is determinedby fluorescence microscopy, electron microscopy, x-ray crystallography,or electron crystallography.
 37. (canceled)
 38. (canceled) 39.(canceled)
 40. (canceled)
 41. A method for screening a test compound,comprising: contacting said test compound with an ordered structure; andanalyzing the results of the interaction of said test compound and theordered structure, such that said test compound is screened.
 42. Themethod of claim 41, wherein said ordered structure is mounted on a solidsupport.
 43. (canceled)
 44. The method of claim 41, wherein said orderedstructure comprises a membrane protein, a cellular receptor, an orphanreceptor, receptor tyrosine kinase, an EPH receptor, an ion channel, acytokine receptor, an multisubunit immune recognition receptor, achemokine receptor, a growth factor receptor, or a G-protein coupledreceptor.
 45. The method of claim 41, wherein said test compound is anagonist, antagonist, inhibitor, or activator.
 46. The method of claim41, wherein said analysis comprises analyzing a shape change of saidprotein.
 47. The method of claim 46, wherein said shape changescorresponds to the multimerization of said membrane protein with itselfor with other membrane proteins.
 48. (canceled)
 49. A protein chip,comprising a solid support and at least one ordered structure of anamphiphilic molecules.
 50. (canceled)
 51. The protein chip of claim 49,wherein said amphiphilic molecule is a membrane protein, a cellularreceptor, an orphan receptor, receptor tyrosine kinase, an EPH receptor,an ion channel, a cytokine receptor, an multisubunit immune recognitionreceptor, a chemokine receptor, a growth factor receptor, or a G-proteincoupled receptor.
 52. The protein chip of claim 49, wherein said proteinchip comprises two or more ordered structures.
 53. (canceled)
 54. Theprotein chip of claim 49, wherein said ordered structure is fabricatedby planar membrane compression. 55.-58. (canceled)
 59. A method fordetermining the structure of a protein, comprising: expressing saidprotein in a cell; obtaining said protein from said cell; applying saidprotein to an interface; compressing said protein on said interface toan appropriate pressure, such that an ordered structure of said proteinis formed; and analyzing said ordered structure such that the structureof said protein is determined.
 60. The method of claim 59, wherein saidprotein is a membrane protein, a cellular receptor, an orphan receptor,receptor tyrosine kinase, an EPH receptor, an ion channel, a cytokinereceptor, an multisubunit immune recognition receptor, a chemokinereceptor, a growth factor receptor, or a G-protein coupled receptor. 61.The method of claim 59, wherein the structure of said protein isdetermined using diffraction by electromagnetic radiation. 62.(canceled)
 63. The protein chip of claim 52, comprising a plurality ofordered structures in discrete wells, wherein said ordered structuresare fabricated by planar membrane compression.